[English] 日本語
Yorodumi
- PDB-7nfm: An octameric barrel state of a de novo coiled-coil assembly: CC-T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nfm
TitleAn octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L21K.
ComponentsCC-Type2-(LaId)4-L21K
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Differential sensing with arrays of de novo designed peptide assemblies.
Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. ...Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. / Brady, R.L. / Tew, D. / Wood, C.W. / Woolfson, D.N.
History
DepositionFeb 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn.ambient_temp
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Type2-(LaId)4-L21K
B: CC-Type2-(LaId)4-L21K
C: CC-Type2-(LaId)4-L21K
D: CC-Type2-(LaId)4-L21K
E: CC-Type2-(LaId)4-L21K
F: CC-Type2-(LaId)4-L21K
G: CC-Type2-(LaId)4-L21K
H: CC-Type2-(LaId)4-L21K
I: CC-Type2-(LaId)4-L21K
J: CC-Type2-(LaId)4-L21K
K: CC-Type2-(LaId)4-L21K
L: CC-Type2-(LaId)4-L21K
M: CC-Type2-(LaId)4-L21K
N: CC-Type2-(LaId)4-L21K
O: CC-Type2-(LaId)4-L21K
P: CC-Type2-(LaId)4-L21K


Theoretical massNumber of molelcules
Total (without water)52,01416
Polymers52,01416
Non-polymers00
Water4,324240
1
A: CC-Type2-(LaId)4-L21K
B: CC-Type2-(LaId)4-L21K
C: CC-Type2-(LaId)4-L21K
D: CC-Type2-(LaId)4-L21K
E: CC-Type2-(LaId)4-L21K
F: CC-Type2-(LaId)4-L21K
G: CC-Type2-(LaId)4-L21K
H: CC-Type2-(LaId)4-L21K


Theoretical massNumber of molelcules
Total (without water)26,0078
Polymers26,0078
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-112 kcal/mol
Surface area11940 Å2
MethodPISA
2
I: CC-Type2-(LaId)4-L21K
J: CC-Type2-(LaId)4-L21K
K: CC-Type2-(LaId)4-L21K
L: CC-Type2-(LaId)4-L21K
M: CC-Type2-(LaId)4-L21K
N: CC-Type2-(LaId)4-L21K
O: CC-Type2-(LaId)4-L21K
P: CC-Type2-(LaId)4-L21K


Theoretical massNumber of molelcules
Total (without water)26,0078
Polymers26,0078
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-114 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.928, 47.958, 72.148
Angle α, β, γ (deg.)70.570, 70.630, 90.100
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116B
216C
117B
217D
118B
218E
119B
219F
120B
220G
121B
221H
122B
222I
123B
223J
124B
224K
125B
225L
126B
226M
127B
227N
128B
228O
129B
229P
130C
230D
131C
231E
132C
232F
133C
233G
134C
234H
135C
235I
136C
236J
137C
237K
138C
238L
139C
239M
140C
240N
141C
241O
142C
242P
143D
243E
144D
244F
145D
245G
146D
246H
147D
247I
148D
248J
149D
249K
150D
250L
151D
251M
152D
252N
153D
253O
154D
254P
155E
255F
156E
256G
157E
257H
158E
258I
159E
259J
160E
260K
161E
261L
162E
262M
163E
263N
164E
264O
165E
265P
166F
266G
167F
267H
168F
268I
169F
269J
170F
270K
171F
271L
172F
272M
173F
273N
174F
274O
175F
275P
176G
276H
177G
277I
178G
278J
179G
279K
180G
280L
181G
281M
182G
282N
183G
283O
184G
284P
185H
285I
186H
286J
187H
287K
188H
288L
189H
289M
190H
290N
191H
291O
192H
292P
193I
293J
194I
294K
195I
295L
196I
296M
197I
297N
198I
298O
199I
299P
1100J
2100K
1101J
2101L
1102J
2102M
1103J
2103N
1104J
2104O
1105J
2105P
1106K
2106L
1107K
2107M
1108K
2108N
1109K
2109O
1110K
2110P
1111L
2111M
1112L
2112N
1113L
2113O
1114L
2114P
1115M
2115N
1116M
2116O
1117M
2117P
1118N
2118O
1119N
2119P
1120O
2120P

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 30 / Label seq-ID: 2 - 31

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18AA
28II
19AA
29JJ
110AA
210KK
111AA
211LL
112AA
212MM
113AA
213NN
114AA
214OO
115AA
215PP
116BB
216CC
117BB
217DD
118BB
218EE
119BB
219FF
120BB
220GG
121BB
221HH
122BB
222II
123BB
223JJ
124BB
224KK
125BB
225LL
126BB
226MM
127BB
227NN
128BB
228OO
129BB
229PP
130CC
230DD
131CC
231EE
132CC
232FF
133CC
233GG
134CC
234HH
135CC
235II
136CC
236JJ
137CC
237KK
138CC
238LL
139CC
239MM
140CC
240NN
141CC
241OO
142CC
242PP
143DD
243EE
144DD
244FF
145DD
245GG
146DD
246HH
147DD
247II
148DD
248JJ
149DD
249KK
150DD
250LL
151DD
251MM
152DD
252NN
153DD
253OO
154DD
254PP
155EE
255FF
156EE
256GG
157EE
257HH
158EE
258II
159EE
259JJ
160EE
260KK
161EE
261LL
162EE
262MM
163EE
263NN
164EE
264OO
165EE
265PP
166FF
266GG
167FF
267HH
168FF
268II
169FF
269JJ
170FF
270KK
171FF
271LL
172FF
272MM
173FF
273NN
174FF
274OO
175FF
275PP
176GG
276HH
177GG
277II
178GG
278JJ
179GG
279KK
180GG
280LL
181GG
281MM
182GG
282NN
183GG
283OO
184GG
284PP
185HH
285II
186HH
286JJ
187HH
287KK
188HH
288LL
189HH
289MM
190HH
290NN
191HH
291OO
192HH
292PP
193II
293JJ
194II
294KK
195II
295LL
196II
296MM
197II
297NN
198II
298OO
199II
299PP
1100JJ
2100KK
1101JJ
2101LL
1102JJ
2102MM
1103JJ
2103NN
1104JJ
2104OO
1105JJ
2105PP
1106KK
2106LL
1107KK
2107MM
1108KK
2108NN
1109KK
2109OO
1110KK
2110PP
1111LL
2111MM
1112LL
2112NN
1113LL
2113OO
1114LL
2114PP
1115MM
2115NN
1116MM
2116OO
1117MM
2117PP
1118NN
2118OO
1119NN
2119PP
1120OO
2120PP

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120

-
Components

#1: Protein/peptide
CC-Type2-(LaId)4-L21K


Mass: 3250.893 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 100 mM sodium citrate tribasic dihydrate, 50 mM sodium 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonate (sodium ...Details: After 1:1 dilution with the peptide solution, the resulting conditions were 100 mM sodium citrate tribasic dihydrate, 50 mM sodium 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonate (sodium HEPES) and 10% v/v 2-propanol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→44.9 Å / Num. obs: 95381 / % possible obs: 94.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.45-1.473.50.7271.746000.7520.4530.85993.1
7.94-44.93.40.06223.35850.9920.0380.07396.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSJan 31, 2020data reduction
XSCALEJan 31, 2020data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.45→33.93 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.915 / SU B: 1.977 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 1885 2 %RANDOM
Rwork0.217 ---
obs0.2177 93225 94.66 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 88.95 Å2 / Biso mean: 27.283 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å2-0.48 Å20.72 Å2
2--2.22 Å20.76 Å2
3----2.26 Å2
Refinement stepCycle: final / Resolution: 1.45→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 0 240 3904
Biso mean---38.54 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134284
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174601
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.6355785
X-RAY DIFFRACTIONr_angle_other_deg1.4481.59310721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2155588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13626.606165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10815958
X-RAY DIFFRACTIONr_chiral_restr0.0820.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A9710.1
12B9710.1
21A9900.06
22C9900.06
31A9670.11
32D9670.11
41A9910.06
42E9910.06
51A9650.1
52F9650.1
61A9900.04
62G9900.04
71A9680.1
72H9680.1
81A9920.05
82I9920.05
91A9690.1
92J9690.1
101A9920.06
102K9920.06
111A9680.09
112L9680.09
121A9890.05
122M9890.05
131A9670.1
132N9670.1
141A9910.05
142O9910.05
151A9730.09
152P9730.09
161B9010.1
162C9010.1
171B9210.07
172D9210.07
181B8900.11
182E8900.11
191B9210.06
192F9210.06
201B8890.1
202G8890.1
211B9240.06
212H9240.06
221B8930.1
222I8930.1
231B9250.07
232J9250.07
241B8880.1
242K8880.1
251B9200.06
252L9200.06
261B8920.09
262M8920.09
271B9230.06
272N9230.06
281B8920.1
282O8920.1
291B9230.06
292P9230.06
301C9960.11
302D9960.11
311C10200.04
312E10200.04
321C9950.11
322F9950.11
331C10120.05
332G10120.05
341C9990.1
342H9990.1
351C10210.04
352I10210.04
361C9990.11
362J9990.11
371C10160.05
372K10160.05
381C9970.1
382L9970.1
391C10130.05
392M10130.05
401C9960.11
402N9960.11
411C10150.06
412O10150.06
421C10050.09
422P10050.09
431D9450.1
432E9450.1
441D9690.05
442F9690.05
451D9400.1
452G9400.1
461D9670.04
462H9670.04
471D9460.11
472I9460.11
481D9680.03
482J9680.03
491D9400.11
492K9400.11
501D9640.05
502L9640.05
511D9420.1
512M9420.1
521D9660.05
522N9660.05
531D9420.1
532O9420.1
541D9710.05
542P9710.05
551E9680.11
552F9680.11
561E9910.05
562G9910.05
571E9720.1
572H9720.1
581E9990.05
582I9990.05
591E9710.11
592J9710.11
601E9950.05
602K9950.05
611E9710.1
612L9710.1
621E9910.06
622M9910.06
631E9700.11
632N9700.11
641E9930.06
642O9930.06
651E9760.1
652P9760.1
661F9120.11
662G9120.11
671F9560.06
672H9560.06
681F9190.11
682I9190.11
691F9570.07
692J9570.07
701F9120.11
702K9120.11
711F9550.06
712L9550.06
721F9150.1
722M9150.1
731F9590.02
732N9590.02
741F9140.11
742O9140.11
751F9450.06
752P9450.06
761G9700.1
762H9700.1
771G9940.06
772I9940.06
781G9710.11
782J9710.11
791G9900.06
792K9900.06
801G9720.09
802L9720.09
811G9910.05
812M9910.05
821G9690.1
822N9690.1
831G9910.06
832O9910.06
841G9730.1
842P9730.1
851H9390.1
852I9390.1
861H9650.05
862J9650.05
871H9320.1
872K9320.1
881H9700.03
882L9700.03
891H9340.09
892M9340.09
901H9640.06
902N9640.06
911H9340.09
912O9340.09
921H9610.04
922P9610.04
931I10080.11
932J10080.11
941I10240.06
942K10240.06
951I10080.09
952L10080.09
961I10210.06
962M10210.06
971I10070.11
972N10070.11
981I10220.06
982O10220.06
991I10110.1
992P10110.1
1001J9280.1
1002K9280.1
1011J9560.07
1012L9560.07
1021J9300.1
1022M9300.1
1031J9620.07
1032N9620.07
1041J9310.1
1042O9310.1
1051J9510.05
1052P9510.05
1061K9680.1
1062L9680.1
1071K9880.06
1072M9880.06
1081K9670.11
1082N9670.11
1091K9900.07
1092O9900.07
1101K9730.1
1102P9730.1
1111L9350.08
1112M9350.08
1121L9650.04
1122N9650.04
1131L9340.09
1132O9340.09
1141L9630.02
1142P9630.02
1151M10040.09
1152N10040.09
1161M10250.03
1162O10250.03
1171M10100.08
1172P10100.08
1181N9160.11
1182O9160.11
1191N9450.06
1192P9450.06
1201O9790.09
1202P9790.09
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 135 -
Rwork0.426 6645 -
all-6780 -
obs--92.67 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more