[English] 日本語
Yorodumi
- PDB-6zt1: Two states of a de novo hexameric coiled coil assembly CC-Type2-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zt1
TitleTwo states of a de novo hexameric coiled coil assembly CC-Type2-(LaIdGe)4
ComponentsCC-Type2-(LaIdGe)4
KeywordsDE NOVO PROTEIN / coiled coil / de novo peptide / multi-state
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsRhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
CitationJournal: Nat Commun / Year: 2021
Title: Structural resolution of switchable states of a de novo peptide assembly.
Authors: Dawson, W.M. / Lang, E.J.M. / Rhys, G.G. / Shelley, K.L. / Williams, C. / Brady, R.L. / Crump, M.P. / Mulholland, A.J. / Woolfson, D.N.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 9, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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-(LaIdGe)4
B: CC-Type2-(LaIdGe)4
C: CC-Type2-(LaIdGe)4
D: CC-Type2-(LaIdGe)4
E: CC-Type2-(LaIdGe)4
F: CC-Type2-(LaIdGe)4
G: CC-Type2-(LaIdGe)4
H: CC-Type2-(LaIdGe)4
I: CC-Type2-(LaIdGe)4
J: CC-Type2-(LaIdGe)4
K: CC-Type2-(LaIdGe)4
L: CC-Type2-(LaIdGe)4


Theoretical massNumber of molelcules
Total (without water)38,62412
Polymers38,62412
Non-polymers00
Water2,684149
1
A: CC-Type2-(LaIdGe)4
B: CC-Type2-(LaIdGe)4
C: CC-Type2-(LaIdGe)4
D: CC-Type2-(LaIdGe)4
E: CC-Type2-(LaIdGe)4
F: CC-Type2-(LaIdGe)4


Theoretical massNumber of molelcules
Total (without water)19,3126
Polymers19,3126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-87 kcal/mol
Surface area9770 Å2
MethodPISA
2
G: CC-Type2-(LaIdGe)4
H: CC-Type2-(LaIdGe)4
I: CC-Type2-(LaIdGe)4
J: CC-Type2-(LaIdGe)4
K: CC-Type2-(LaIdGe)4
L: CC-Type2-(LaIdGe)4


Theoretical massNumber of molelcules
Total (without water)19,3126
Polymers19,3126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-104 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 128.100, 56.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name N or name...
21(chain B and ((resid 3 and (name N or name...
31(chain C and ((resid 3 and (name N or name...
41(chain D and ((resid 3 and (name N or name...
51(chain E and ((resid 3 and (name N or name...
61(chain F and ((resid 3 and (name N or name...
71(chain G and ((resid 3 and (name O or name...
81(chain H and ((resid 3 and (name N or name...
91(chain J and ((resid 3 and (name N or name...
101(chain K and ((resid 3 and (name O or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILE(chain A and ((resid 3 and (name N or name...AA34
12ACEACEGLYGLY(chain A and ((resid 3 and (name N or name...AA0 - 301 - 31
13ACEACEGLYGLY(chain A and ((resid 3 and (name N or name...AA0 - 301 - 31
14ACEACEGLYGLY(chain A and ((resid 3 and (name N or name...AA0 - 301 - 31
15ACEACEGLYGLY(chain A and ((resid 3 and (name N or name...AA0 - 301 - 31
16ACEACEGLYGLY(chain A and ((resid 3 and (name N or name...AA0 - 301 - 31
21ILEILEILEILE(chain B and ((resid 3 and (name N or name...BB34
22ACEACEGLYGLY(chain B and ((resid 3 and (name N or name...BB0 - 301 - 31
23ACEACEGLYGLY(chain B and ((resid 3 and (name N or name...BB0 - 301 - 31
24ACEACEGLYGLY(chain B and ((resid 3 and (name N or name...BB0 - 301 - 31
25ACEACEGLYGLY(chain B and ((resid 3 and (name N or name...BB0 - 301 - 31
26ACEACEGLYGLY(chain B and ((resid 3 and (name N or name...BB0 - 301 - 31
31ILEILEILEILE(chain C and ((resid 3 and (name N or name...CC34
32ACEACEGLYGLY(chain C and ((resid 3 and (name N or name...CC0 - 301 - 31
33ACEACEGLYGLY(chain C and ((resid 3 and (name N or name...CC0 - 301 - 31
34ACEACEGLYGLY(chain C and ((resid 3 and (name N or name...CC0 - 301 - 31
35ACEACEGLYGLY(chain C and ((resid 3 and (name N or name...CC0 - 301 - 31
36ACEACEGLYGLY(chain C and ((resid 3 and (name N or name...CC0 - 301 - 31
41ILEILEILEILE(chain D and ((resid 3 and (name N or name...DD34
42ACEACEGLYGLY(chain D and ((resid 3 and (name N or name...DD0 - 301 - 31
43ACEACEGLYGLY(chain D and ((resid 3 and (name N or name...DD0 - 301 - 31
44ACEACEGLYGLY(chain D and ((resid 3 and (name N or name...DD0 - 301 - 31
45ACEACEGLYGLY(chain D and ((resid 3 and (name N or name...DD0 - 301 - 31
46ACEACEGLYGLY(chain D and ((resid 3 and (name N or name...DD0 - 301 - 31
51ILEILEILEILE(chain E and ((resid 3 and (name N or name...EE34
52ACEACELYSLYS(chain E and ((resid 3 and (name N or name...EE0 - 291 - 30
53ACEACELYSLYS(chain E and ((resid 3 and (name N or name...EE0 - 291 - 30
54ACEACELYSLYS(chain E and ((resid 3 and (name N or name...EE0 - 291 - 30
55ACEACELYSLYS(chain E and ((resid 3 and (name N or name...EE0 - 291 - 30
56ACEACELYSLYS(chain E and ((resid 3 and (name N or name...EE0 - 291 - 30
61ILEILEILEILE(chain F and ((resid 3 and (name N or name...FF34
62ACEACEGLYGLY(chain F and ((resid 3 and (name N or name...FF0 - 301 - 31
63ACEACEGLYGLY(chain F and ((resid 3 and (name N or name...FF0 - 301 - 31
64ACEACEGLYGLY(chain F and ((resid 3 and (name N or name...FF0 - 301 - 31
65ACEACEGLYGLY(chain F and ((resid 3 and (name N or name...FF0 - 301 - 31
66ACEACEGLYGLY(chain F and ((resid 3 and (name N or name...FF0 - 301 - 31
71ILEILEILEILE(chain G and ((resid 3 and (name O or name...GG34
72GLUGLUGLYGLY(chain G and ((resid 3 and (name O or name...GG2 - 303 - 31
73GLUGLUGLYGLY(chain G and ((resid 3 and (name O or name...GG2 - 303 - 31
74GLUGLUGLYGLY(chain G and ((resid 3 and (name O or name...GG2 - 303 - 31
75GLUGLUGLYGLY(chain G and ((resid 3 and (name O or name...GG2 - 303 - 31
76GLUGLUGLYGLY(chain G and ((resid 3 and (name O or name...GG2 - 303 - 31
81ILEILEILEILE(chain H and ((resid 3 and (name N or name...HH34
82GLYGLYGLYGLY(chain H and ((resid 3 and (name N or name...HH1 - 302 - 31
83GLYGLYGLYGLY(chain H and ((resid 3 and (name N or name...HH1 - 302 - 31
84GLYGLYGLYGLY(chain H and ((resid 3 and (name N or name...HH1 - 302 - 31
85GLYGLYGLYGLY(chain H and ((resid 3 and (name N or name...HH1 - 302 - 31
86GLYGLYGLYGLY(chain H and ((resid 3 and (name N or name...HH1 - 302 - 31
91ILEILEILEILE(chain J and ((resid 3 and (name N or name...JJ34
92ACEACEGLYGLY(chain J and ((resid 3 and (name N or name...JJ0 - 301 - 31
93ACEACEGLYGLY(chain J and ((resid 3 and (name N or name...JJ0 - 301 - 31
94ACEACEGLYGLY(chain J and ((resid 3 and (name N or name...JJ0 - 301 - 31
95ACEACEGLYGLY(chain J and ((resid 3 and (name N or name...JJ0 - 301 - 31
96ACEACEGLYGLY(chain J and ((resid 3 and (name N or name...JJ0 - 301 - 31
101ILEILEILEILE(chain K and ((resid 3 and (name O or name...KK34
102GLYGLYLYSLYS(chain K and ((resid 3 and (name O or name...KK1 - 292 - 30
103GLYGLYLYSLYS(chain K and ((resid 3 and (name O or name...KK1 - 292 - 30
104GLYGLYLYSLYS(chain K and ((resid 3 and (name O or name...KK1 - 292 - 30
105GLYGLYLYSLYS(chain K and ((resid 3 and (name O or name...KK1 - 292 - 30
106GLYGLYLYSLYS(chain K and ((resid 3 and (name O or name...KK1 - 292 - 30

-
Components

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


Mass: 3218.627 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M Sodium HEPES, 5% w/v PEG 4000 and 5% v/v 2-Propanol at a pH of 7 (values based on 1:1 dilution of ProPlex B6 crystallisation condition with peptide solution)

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.01→58.92 Å / Num. obs: 29226 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.142 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
2.01-2.0813.31.6381.828760.5650.8580.4651.70499.9
8.99-58.929.80.05729.83860.0190.0696.8

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→56.53 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1396 4.78 %
Rwork0.2071 --
obs0.2097 29204 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.77 Å2 / Biso mean: 45.6945 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 2.01→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 0 149 2785
Biso mean---51.69 -
Num. residues----364
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A291X-RAY DIFFRACTION11.478TORSIONAL
12B291X-RAY DIFFRACTION11.478TORSIONAL
13C291X-RAY DIFFRACTION11.478TORSIONAL
14D291X-RAY DIFFRACTION11.478TORSIONAL
15E291X-RAY DIFFRACTION11.478TORSIONAL
16F291X-RAY DIFFRACTION11.478TORSIONAL
17G291X-RAY DIFFRACTION11.478TORSIONAL
18H291X-RAY DIFFRACTION11.478TORSIONAL
19J291X-RAY DIFFRACTION11.478TORSIONAL
110K291X-RAY DIFFRACTION11.478TORSIONAL
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1642-0.41260.10561.81430.51310.8674-0.4673-0.157-0.11461.51660.73850.96980.016-0.20380.01850.4410.11950.09040.39420.07030.261525.400741.47486.3684
21.20440.549-0.09990.3153-0.06580.1292-0.01010.08250.18820.10610.31610.6450.0203-0.15640.00480.33220.00640.00620.38890.07450.319518.962941.8192-0.7766
3-0.3520.86890.54350.59710.72190.499-0.42620.10580.3272-1.25120.67761.00950.2111-0.22270.00110.3564-0.0301-0.0260.42840.07340.383821.919842.0121-9.3143
40.3411-0.2473-0.37221.2453-0.1930.7957-0.42460.0727-0.2626-0.84920.6082-1.11740.0006-0.00590.00910.321-0.04740.02350.3765-0.00580.269430.987541.19-11.7317
52.07910.3738-0.56951.0039-0.64590.3695-0.22520.049-0.2233-0.50740.4463-1.4686-0.09890.2545-0.00090.33290.07960.00880.346-0.020.332937.609841.0198-4.0926
6-0.25790.67080.12921.5592-0.95620.5573-0.2663-0.23370.01431.63060.3748-0.60960.02550.1030.00140.38580.1022-0.05070.386-0.01560.371634.74441.01234.5904
71.9716-1.13960.68950.9111-0.15250.8477-0.06540.4216-0.2645-1.0010.255-0.06410.02820.04110.00450.37360.0147-0.00580.3377-0.06840.333127.968123.162618.6184
82.9213-0.75410.56033.47131.65891.82860.35280.3881-0.301-1.5206-0.2632-0.5248-0.51870.0353-0.04330.23610.03070.05220.2785-0.1020.329135.789722.853622.1296
92.28950.2407-0.14330.9197-0.98330.98590.37270.0418-0.11730.1809-0.1722-1.54840.0810.0847-0.0050.25450.0126-0.05650.2834-0.02570.408738.630721.943730.0571
102.06691.08840.62970.70180.6860.99890.0833-0.5002-0.20171.0310.0153-0.18460.1088-0.06650.00640.3378-0.0207-0.00360.24550.04880.285827.771523.563632.5873
111.4655-0.10130.11110.2320.04240.96140.2122-0.2302-0.26840.1912-0.00811.23970.0829-0.19430.0010.2957-0.0503-0.02140.31130.0650.402720.688722.618527.6837
124.45840.7660.95630.7710.65781.13120.5120.1645-0.15150.25430.02351.5688-0.1023-0.32070.04030.31390.0068-0.04180.3246-0.02220.429417.571922.674120.4207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A1 - 30
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 30 )B1 - 30
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 30 )C1 - 30
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 30 )D1 - 30
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 29 )E1 - 29
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 30 )F1 - 30
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 30 )G2 - 30
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 30 )H1 - 30
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 30 )I1 - 30
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 30 )J1 - 30
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 29 )K1 - 29
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 29 )L1 - 29

+
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://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