Structures - CASP13

1.

T0949

D1: 43-181 (139)

D9: 33-183 (151)

-

2

A

ok

-

183

129

1-42, 96-105, 182-183

1

-

Week indication of signal peptide in 1-32 (SignalP).
# Measure  Position  Value    Cutoff   signal peptide?
  max. C    33       0.439
  max. Y    33       0.374
  max. S    18       0.630
  mean S     1-32    0.418
       D     1-32    0.392   0.500   NO
Name=T0949	SP='NO' D=0.392 D-cutoff=0.500 Networks=SignalP-TM

2.

T0950

D1: 12-353 (342)

-

4

A

3 regions of 2aa deviating: 99,100; 217,218; 241,242. All left in the structure.

-

353

342

1-11

1

-

-

3.

T0951

D1: 8-273 (266)

-

1

A

-

276

266

1-7,274-276

1

-

-

4.

T0952

-

35

-

-

5.

T0953s1

D1: 6-72 (67)

-

3

B

Distant amino acids: 4, 5 (res.1-3 missing in chains A and C). Residues 1-5 deleted from the evaluation domain D1.

-

321

72

-

1

-

-

6.

T0953s2

D1: 2-45 (44)

D2: 46-114,131-151,229-249 (111)

D3: 115-130,152-228 (93)

-

1

D

-

321

248

1

2 DomainParser: dpar 248 2 (2-45) (46-249) DDomain: AUTHORS-trained parameters 1 2 - 45 2 46 - 249

-

-

7.

T0954

D1: 9-45,52-350 (336)

-

3

A

Distant amino acids: loop 46-51, 175-176 in chain B. Chain A selected and res. 46-51 deleted from D1.

-

350

342

1-8

3 or 1? DomainParser: dpar 342 3 (9-74;272-350) (75-163) (164-271) DDomain: AUTHORS-trained parameters 1 9-350

295G->A

Changed 295ALA->GLY

8.

T0955

D1: 1-41 (41)

NMR

-

20 mdls

A

ok

-

41

-

1

-

-

9.

T0956

-

178

-

-

10.

T0957s1

D1: 2-37,92-163 (108)

D2: 38-91 (54)

-

2

A

Distant amino acids: 161, 163

-

327

162

1

-

MSE -> MET

11.

T0957s2

D1: 7-161 (155)

-

2

C

Distant amino acids: 162-164 Deleted from D2.

-

327

158

1-6

1 or 2? DomainParser: dpar 158 2 (7-82) (83-164) DDomain: AUTHORS-trained parameters 1 7 - 164

MSE -> MET

-

12.

T0958

D1: 5-81 (77)

-

2

A

Res. 82 and 83 differ in two chains; trimmed off.

-

96

79

1-4,82-96

1

Mse->Met

-

13.

T0959

D1: 1-26,32-169,174-189 (180)

-

2

A

Distant amino acids: 27-31, 170-173. Trimmed off D1.

-

189

-

DomainParser: dpar 189 1

-

Ignore difference in chains

14.

T0960

D1: 11-42 (32)

D2: 43-126 (84)

D3: 127-215 (89)

D4: 216-279 (64)

D5: 280-384 (105)

-

6

A

(A,B,C) (D,E,F)

-

384

374

1-10

DomainParser: 3: (11-129) (130-254) (255-384)

-

Substantial variation in chains if superimpose the whole thing (due to slight change in inter-domain angles in the elongated structure of each chain). 

After splitting into domains first, there is perfect match between the structures in all 6 chains (see files e.g. T0960-D2.6chains.pdb in CHAIN_SUPERPOSITIONS)

15.

T0961

D1: 3-505 (503)

-

2

A

Almost identical

FAD

505

503

1,2

1 or 2 (3-290)(291-505)

-

-

16.

T0962

D1: 2-178 (177)

-

1

A

-

220

177

1,179-220

1

-

-

17.

T0963

D1: 9-39 (31)

D2: 40-121 (82)

D3: 122-214 (93)

D4: 215-278 (64)

D5: 279-372 (94)

-

6

A

(A,B,C) (D,E,F)

-

372

364

1-8

DomainParser: 3 : (9-121) (122-244) (245-372)

-

Substantial variation in chains if superimpose the whole thing (due to slight change in inter-domain angles in the elongated structure of each chain). 

After splitting into domains first, there is perfect match between the structures in all 6 chains (see files e.g. T0960-D2.6chains.pdb in CHAIN_SUPERPOSITIONS)

18.

T0964

D1: 90-184 (95)

-

1

A

-

184

95

1-89

1

DIFF: 97: V-A; 98: K-R; 105: D-N; 111: V-I; 123: V-I; 134: A-T; 146: H-N; 150: H-Q; 172: Q-L; 175: V-I; 182: T-M;

-

19.

T0965

D1: 14-326 (313)

-

2

A

DIstant res. 285

LIG, NDP

334

313

1-13,327-334

DomainParser: dpar 313 1 DDomain: AUTHORS-trained parameters 1 14 - 91 2 92 - 191 3 192 - 326

-

-

20.

T0966

D1: 1-492 (492)

D9: 135-235 (101)

-

2

A

Diff. 274,275

GOL, SO4, CL

494

492

493,494

DomainParser: dpar 492 3 (1-110) (111-260) (261-492) DDomain: AUTHORS-trained parameters 1 1 - 74 2 75 - 125 3 126 - 248 4 249 - 492

-

-

21.

T0967

D1: 1-79 (79)

-

6

A

Distant amino acids: 80, 81

-

81

79

-

1

-

Deleted distant C_term residues 80 and 81.

22.

T0968s1

D1: 5-123 (119)

-

4

A

ACEG

-

242

119

1-5, 124-126

1

-

-

23.

T0968s2

D1: 1-116 (116)

-

B

BDFH

-

242

116

DomainParser: dpar 116 2 (1-75) (76-116) DDomain: 1 1 - 116

-

-

24.

T0969

D1: 133-486 (354)

-

1

A

-

487

354

1-132, 487

1

-

-

25.

T0970

D1: 1-97 (97)

-

4

A

Chain D most different. A,B most similar. Distant res. in AB: 39-46; 80-83 are trimmed off.

-

97

-

1

-

Target was released without disordered regions 271-232, 257-263, 301-305 in original numbering

26.

T0971

D1: 57-186 (130)

-

1

A

-

186

130

1-56

1

-

-

27.

T0972

-

106

-

-

28.

T0973

D1: 1-59,66-83,96-146 (128)

-

3

A

Distant amino acids: 60-65, 84-95. Trimmed off.

-

146

141

chain A: 60-64

1

Chain C: DIFF: 80: I-Q;

In the loop 84-95 chain B is very different, chains A and C are similar.

29.

T0974s1

D1: 2-70 (69)

-

1

B

-

167

69

1,71-72

1

-

-

30.

T0974s2

D1: 1-80 (80)

-

A

-

167

80

81-95

1

-

-

31.

T0975

D1: 36-328 (293)

-

1

A

-

343

281

1-35, 77-88, 329-343

1

-

-

32.

T0976

D1: 9-128 (120)

D2: 129-252 (124)

-

2

A

ok

-

252

250

1-2

2 (3-125) (126-252)

mse-met

-

33.

T0977

D1: 59-359 (301)

D2: 360-563 (204)

-

3

A

Long helix (17-57) has different relative orientation in 3 chains (with respect to the rest of the structure)

-

566

547

1-16,564-566

Suggest 4 domains: D1:17-58, D2:59-359, D3:360-466, D4:467-563

MSE->MET

-

34.

T0978

D1: 2-414 (413)

-

1

B

-

416

409

1,415-416

2 (2-257)(258-414)

-

A better refined structure is processed on Sep. 27.

35.

T0979

D1: 6-97 (92)

-

3

A

ideal

-

98

92

1-5,98

Domain parsers - 1 domain Suggest 3 domains (middle one of interest): D1:6-33, D2:34-70, D3:71-97

-

-

36.

T0980s1

D1: 1-105 (105)

-

A

OK

-

163

104

36,106-111

1

-

-

37.

T0980s2

D1: 6-36 (31)

-

B

ok

-

163

31

1-5,37-52

1

-

-

38.

T0981

D1: 34-119 (86)

D2: 120-190,394-402 (80)

D3: 191-393 (203)

D4: 403-513 (111)

D5: 514-640 (127)

-

6

A

perfect

-

640

607

1-33

DomainParser: 5 (34-119) (120-190;392-402) (403-513) (191-391) (514-640)

mse->met

-

39.

T0982

D1: 11-145 (135)

D2: 146-277 (132)

-

1

A

-

283

267

1-10, 278-283

2: (11-145) (146-277)

-

-

40.

T0983

D1: 1-236 (236)

-

2

A

142:B - 142:A - 5.181 143:B - 143:A - 9.332 144:B - 144:A - 8.609 145:B - 145:A - 8.277 146:B - 146:A - 5.036 155:B - 155:A - 3.691 160:B - 160:A - 4.668 161:B - 161:A - 4.852 162:B - 162:A - 4.778 163:B - 163:A - 4.357 164:B - 164:A - 4.395 182:B - 182:A - 4.037 183:B - 183:A - 5.158 184:B - 184:A - 5.435 185:B - 185:A - 6.416 186:B - 186:A - 7.091 187:B - 187:A - 8.825 188:B - 188:A - 8.503 189:B - 189:A - 7.684 190:B - 190:A - 6.708 191:B - 191:A - 6.008 192:B - 192:A - 5.089 193:B - 193:A - 4.527 194:B - 194:A - 3.596

SAM

245

236

237-245

1 domain?

-

-

41.

T0984

D0: 39-406,417-563,565-700 (651)

D1: 39-406,565-700 (504)

D2: 417-563 (147)

-

2

A

ok

-

752

620

1-38,241-251,347-353,525-537,609-619,701-752

Domain Parser: 1 Ddomain: 1 (39-407,562-700); 2 (408-561)

-

cryo-EM

42.

T0985

D1: 22-863 (842)

-

1

A

-

863

842

1-21

2: (22-352) (353-863)

-

-

43.

T0986s1

D1: 5-96 (92)

-

1

A

-

251

92

1-4

1

mse->met

-

44.

T0986s2

D1: 1-155 (155)

-

1

B

-

251

155

-

1

mse->met

-

45.

T0987

D1: 11-195 (185)

D2: 196-402 (207)

-

1

A

-

405

381

1-10, 363-373, 403-405

2: (11-195)(196-402)

-

-

46.

T0988

-

6

A

identical

-

204

-

1

-

-

47.

T0989

D1: 1-134 (134)

D2: 135-246 (112)

-

6

A

identical

-

246

-

2: (1-134)(135-246)

-

-

48.

T0990

D1: 1-76 (76)

D2: 77-134,348-520 (231)

D3: 135-347 (213)

-

1

A

-

552

-

2: (1-134;348-520)(135-347) ; C-term helix with linker (520-552) clipped off

-

EM structure with quite poor resolution (4A)

49.

T0991

D1: 1-59,67-118 (111)

-

3

A

Distant amino acids: 10-11(chain B), 60-66 (all 3 chains). Res. 60-66 trimmed in D1.

-

118

-

1

-

Chain A is more similar to B and C

50.

T0992

D1: 4-110 (107)

-

1

A

-

126

107

1-3, 111-126

1

-

-

51.

T0993s1

D1: 5-267 (263)

-

2

A

A, C - OK

-

378

263

1-4, 268-269

2? (94-162) (5-93;163-267)

-

-

52.

T0993s2

D1: 12-109 (98)

-

2

B

B,D - OK

-

378

98

1-11

1

-

-

53.

T0994

D8: 1-333 (333)

D9: 334-585 (252)

-

585

-

-

54.

T0995

D1: 3-296 (294)

-

18

A

identical chains

-

330

317

1-2,320-330

1

DIFF: 86: Q-R; 305: H-K; 308: H-K;

-

55.

T0996

D1: 17-123 (107)

D2: 124-250 (127)

D3: 251-350 (100)

D4: 351-483 (133)

D5: 484-604 (121)

D6: 605-708 (104)

D7: 709-848 (140)

-

6

A

OK

-

848

832

1-16

-

From the author:

Attached is the highest resolution composite model.  This is a cryo EM structure, and through masking and focused classification, we have 12+ maps and models, with more than one conformation.  We are still ourselves trying to figure out how we will present it in a paper, and I am not sure if it is practical for you all you compare predictions to multiple models of the same protein?

56.

T0997

D1: 44-228 (185)

-

2

A

ok

-

228

201

1-2,19-43

1

-

-

57.

T0998

D1: 1-166 (166)

-

21

A

similar

-

166

-

1

-

-

58.

T0999

D1: 15-400 (386)

D2: 401-853 (453)

D3: 866-1045 (180)

D4: 1046-1289 (244)

D5: 1290-1577 (288)

-

2

A

Res. 879-998 and 1492-1495 deviate in different chains in the overall superposition. No discrepancy In domain-based superposition (only single res. 879 in D3).

-

1589

1551

1-14, 854-865, 1578-1589

Manual parsing into domains: (15-400) (401-853)(866-1045)(1046-1289)(1290-1491)

-

-

59.

T1000

D0: 10-523 (514)

D1: 10-92 (83)

D2: 93-523 (431)

-

4

C

Deviating res. 10-11 in Domain 1 (not assessed). Single residue differences in positions 206 and 248.

-

523

451

1-9,177-185,212-246,358-376

DDomain: 1 10 - 92 2 93 - 277 3 278 - 523

mse->met

-

60.

T1001

D1: 2-140 (139)

-

6

A

ok

-

140

139

1

-

-

61.

T1002

D0: 1-270 (270)

D1: 1-59 (59)

D2: 60-118 (59)

D3: 127-270 (144)

-

1

A

-

270

271

-

DomainParser: 3 (1-59)(60-126)(127-270)

DIFF: 15: A-S;

-

62.

T1003

D1: 29-465 (437)

-

4

A

Distant amino acids: 69-72 only in chain D. Left in the structure.

PMP

474

434

1-28, 440-442, 466-474

DomainParser: 434 2 (29-83;327-465)(84-326)

-

-

63.

T1004

D1: 66-151 (86)

D2: 152-228 (77)

D3: 229-458 (230)

-

3

A

Distant amino acids: 62-65, 107, 413-416

-

458

397

1-61

4 (manual): (62-151)(152-228) (229-336) (337-458)

-

Deleted 62-65 at the beginning of D1 (monomer). Domain with 413-416 is not evaluated. For oligomers, deleted both deviating regions.

64.

T1005

D1: 39-364 (326)

-

1

A

-

364

326

1-38

1 domain

mse->met

-

65.

T1006

D1: 1-77 (77)

-

2

A

Res. 1-4 in chain A look natural (continuation of the helix), so left in the monomeric target. Deleted from oligomeric. 29:B - 29:A - 3.548

-

79

77

78,79

1

DIFFERENCES: Chain A: 65: R-A; 66: D-A; Chain B: DIFF: 4: G-A; 15: E-A; 28: I-A; 29: G-A; 30: Q-A; 31: K-A; Asked authors to fix, but they sent back structure with the same problems. Changed to the released sequence.

-

66.

T1007

-

149

-

-

67.

T1008

D1: 3-79 (77)

-

20 mdls

Mdl 1A

In the original numbering res. 1-19 and 97 are flexible; in new numbering: res. 1-2, 80 - trimmed off.

-

80

77

-

1

-

Res. 1-2, 80 trimmed off.

68.

T1009

D1: 1-718 (718)

D9: 595-718 (124)

-

2

A

-

718

717

-

DomainParser: dpar 718 3 (1-241) (242-594) (595-718) DDomain: AUTHORS-trained parameters 1 1 - 133 2 134 - 239 3 240 - 484 4 485 - 593 5 594 - 718

-

-

69.

T1010

D1: 1-210 (210)

-

2

A

Distant amino acids: 121, 124

-

210

-

1

-

-

70.

T1011

D1: 55-268,433-520 (302)

D2: 271-430 (160)

-

1

A

-

MIS (misoprostol)

534

444

1-54, 222-232, 469-479, 521-534

2 (55-268;433-520) (271-430)

-

Res. 269,270 and 431,432 are GS linkers between the EP3 receptor and fused T4L lysozyme. THe lysozyme structure is known.

71.

T1012

-

199

-

-

72.

T1013

D1: 39-236,422-511 (288)

-

1

v2_A

Two slightly different variants of structure (depending on ligand). Version v2 selected as main reference structure as having only 1 mutation.

v1: Ago; v2:CYN

537

289

1-38

1

237 A->S

Have structure of the SSTR receptor solved with two different ligands. Both structures are fused to the lysozyme (res. 1000+ in the original structure). Since structure of the lysozyme is known, it is of no interest for evaluation. Prepared two variants of the target (receptor only) for evaluation (v1 with AGO ligand, v2- with CYN). Assessors can use only one set of results, or the best score from 2 datasets.  

The structure with CYN ligand has 1 mutation compared to the original sequence: 237: A-S.
The structure with Ago ligand has quite a few mutations: DIFF: 88: N-D; 170: L-I; 171: L-I; 182: L-V; 189: R-K; 195: N-I; 214: L-I; 217: L-I; 220: L-I; 237: A-S;

73.

T1014

D1: 1-159 (159)

D2: 160-276 (117)

-

1

A

-

276

268

107-114

DomainParser: dpar 268 2 (1-160) (161-276)

-

Relative domain orientation is probably physiologically relevant.

74.

T1015s1

D1: 2-89 (88)

-

2

D

BD - similar

-

218

88

1

1: 2-89

-

-

75.

T1015s2

D1: 1-129 (129)

-

2

A

AC - similar

-

218

129

-

1: 1-129

-

-

76.

T1016

D1: 1-202 (202)

-

4

A

chain D res. 115 115:A - 115:D - 3.504

-

203

202

203

1

mse-met

-

77.

T1017s1

D1: 1-110 (110)

-

2

A

AB - OK

-

240

110

-

1

-

-

78.

T1017s2

D1: 2-129 (128)

-

2

C

CD: res. 100-102 differ and deleted 37:D - 37:C - 3.725 100:D - 100:C - 6.624 101:D - 101:C - 7.228 102:D - 102:C - 5.927

-

240

125

1

1: 2-129

-

-

79.

T1018

D1: 1-334 (334)

-

2

A

OK

DCF, CXS

334

-

1

-

-

80.

T1019s1

D1: 1-58 (58)

-

1

I

-

FE

146

58

-

1

-

-

81.

T1019s2

D1: 1-88 (88)

-

1

A

-

146

88

-

1

-

-

82.

T1020

D1: 191-512 (322)

-

3

A

ok

-

577

313

1-190, 386-394, 513-577

DomainParser: 2 (191-385) (395-512) DDomain: 1 191 - 512

-

cryo EM

83.

T1021s1

D1: 1-149 (149)

-

1

A

-

798

149

-

1 (1-149)

-

From the author:

For the Q6HAD8,Q6HAD7,Q6HAC3 complex : the resolution is not consistent across the whole complex. It is worse for Q6HAC3, especially in the upper region with loops.

84.

T1021s2

D1: 4-352 (349)

-

1

B

-

798

349

1-3, 353-354

DomainParser: dpar 349 1 DDomain: 1 4 - 257 2 258 - 352

-

From the author:

For the Q6HAD8,Q6HAD7,Q6HAC3 complex : the resolution is not consistent across the whole complex. It is worse for Q6HAC3, especially in the upper region with loops.

85.

T1021s3

D1: 4-181 (178)

D2: 195-295 (101)

-

1

C

-

798

275

1-3, 37-39, 93-101, 213-216

DomainParser: dpar 275 1 DDomain: 1 4 - 183 2 184 - 295

-

MISSING res. 131 - corrected

86.

T1022s1

D1: 2-157 (156)

D2: 158-224 (67)

3.3-3.5

EM

-

1

B

-

758

223

1, 225-229

T1022s1 DomainParser: dpar 223 1 DDomain: AUTHORS-trained parameters 1 2 - 167 2 168 - 224

-

From the author:

For the Q6HAD2,Q6HAD1 complex (CASP target H1022) : resolution is 3.3-3.5A, but quite anisotropic. 

The atomic model that you have is not readily fitted in the map. I attach to this email the same PDB, but fitted in the map that you will receive via wetransfer (FOR-CASP_map_2.mrc)
You will see that the maps contain much more than only the provided atomic model. Voxel size of the maps : 0.675A.

I know that the models are probably far from perfect, not only because of the low resolution of the data ...

87.

T1022s2

D1: 3-527 (525)

3.3-3.5

-

1

I

-

758

504

1-2, 134-140, 184-188, 248-256, 528-529

T1022s2 DomainParser: dpar 504 1 DDomain: AUTHORS-trained parameters 1 3 - 96 2 97 - 527

-

AK: Res. 350 to the end seem poorly refined, especially after res. 430 (no secondary structure).

From the author:

For the Q6HAD2,Q6HAD1 complex (CASP target H1022) : resolution is 3.3-3.5A, but quite anisotropic. 

The atomic model that you have is not readily fitted in the map. I attach to this email the same PDB, but fitted in the map that you will receive via wetransfer (FOR-CASP_map_2.mrc)
You will see that the maps contain much more than only the provided atomic model. Voxel size of the maps : 0.675A.

I know that the models are probably far from perfect, not only because of the low resolution of the data ...

88.

T1023s1

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1120

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89.

T1023s2

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1120

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90.

T1023s3

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1120

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