[English] 日本語
Yorodumi
- PDB-7nfj: A heptameric barrel state of a de novo coiled-coil assembly: CC-T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nfj
TitleA heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L28Y.
ComponentsCC-Type2-(LaId)4-L28Y
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Type2-(LaId)4-L28Y
B: CC-Type2-(LaId)4-L28Y
C: CC-Type2-(LaId)4-L28Y
D: CC-Type2-(LaId)4-L28Y
E: CC-Type2-(LaId)4-L28Y
F: CC-Type2-(LaId)4-L28Y
G: CC-Type2-(LaId)4-L28Y


Theoretical massNumber of molelcules
Total (without water)22,9947
Polymers22,9947
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-110 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.539, 130.416, 38.454
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
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

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
17BB
27CC
18BB
28DD
19BB
29EE
110BB
210FF
111BB
211GG
112CC
212DD
113CC
213EE
114CC
214FF
115CC
215GG
116DD
216EE
117DD
217FF
118DD
218GG
119EE
219FF
120EE
220GG
121FF
221GG

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

-
Components

#1: Protein/peptide
CC-Type2-(LaId)4-L28Y


Mass: 3284.887 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
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 50 mM sodium 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonate (sodium HEPES), 5% w/v PEG 8000 and 4% v/v ethylene glycol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.19→45.58 Å / Num. obs: 78107 / % possible obs: 98.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 17.62 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.013 / Rrim(I) all: 0.046 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.19-1.225.80.8931.652510.7230.3970.98291.2
5.32-48.4810.70.04754.510150.9830.020.05198.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
DIALS1.8.3-g908a951f-releasedata reduction
Aimless0.5.32data scaling
xia20.5.482-g030776d9-dials-1.8data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.19→45.53 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.701 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 3764 5 %RANDOM
Rwork0.1675 ---
obs0.1692 71552 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 106.24 Å2 / Biso mean: 28.718 Å2 / Biso min: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å2-0 Å2-0 Å2
2---1.86 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: final / Resolution: 1.19→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 110 1724
Biso mean---48.75 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131746
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171811
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.6362354
X-RAY DIFFRACTIONr_angle_other_deg1.6751.5864194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6125228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44526.08174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21215358
X-RAY DIFFRACTIONr_chiral_restr0.1260.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_rigid_bond_restr5.97533557
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8500.09
12B8500.09
21A8380.1
22C8380.1
31A8410.11
32D8410.11
41A8230.11
42E8230.11
51A8520.09
52F8520.09
61A8290.1
62G8290.1
71B9120.1
72C9120.1
81B9160.08
82D9160.08
91B9130.09
92E9130.09
101B9170.1
102F9170.1
111B9110.07
112G9110.07
121C8410.11
122D8410.11
131C8590.09
132E8590.09
141C8580.12
142F8580.12
151C8570.1
152G8570.1
161D8580.11
162E8580.11
171D8890.11
172F8890.11
181D8770.08
182G8770.08
191E8640.11
192F8640.11
201E8790.09
202G8790.09
211F8160.12
212G8160.12
LS refinement shellResolution: 1.19→1.22 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.507 242 -
Rwork0.466 4371 -
obs--79.6 %

+
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