[English] 日本語
Yorodumi
- PDB-8enz: Crystal structure of alpha-COPI-WD40 domain K15A mutant. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8enz
TitleCrystal structure of alpha-COPI-WD40 domain K15A mutant.
ComponentsPutative coatomer subunit alpha
KeywordsPROTEIN TRANSPORT / COPI / protein trafficking / SARS-CoV-2 spike / dibasic motif
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity / Golgi apparatus / cytoplasm
Similarity search - Function
Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat ...Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ACETYL GROUP / Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsDey, D. / Hasan, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA134274 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150187 United States
CitationJournal: Nat Commun / Year: 2023
Title: A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Authors: Dey, D. / Qing, E. / He, Y. / Chen, Y. / Jennings, B. / Cohn, W. / Singh, S. / Gakhar, L. / Schnicker, N.J. / Pierce, B.G. / Whitelegge, J.P. / Doray, B. / Orban, J. / Gallagher, T. / Hasan, S.S.
History
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative coatomer subunit alpha
B: Putative coatomer subunit alpha
C: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5756
Polymers116,4433
Non-polymers1323
Water13,241735
1
A: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8582
Polymers38,8141
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8582
Polymers38,8141
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8582
Polymers38,8141
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.487, 172.265, 71.483
Angle α, β, γ (deg.)90.000, 99.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Putative coatomer subunit alpha / Alpha-coat protein / Alpha-COP


Mass: 38814.184 Da / Num. of mol.: 3 / Mutation: K15A
Source method: isolated from a genetically manipulated source
Details: Fo-Fc electron density for 172-199 and 332-337 not detected.
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Homo sapiens (human) / References: UniProt: Q96WV5
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.14M Sodium citrate tribasic dihydrate, 18% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2022 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→28.84 Å / Num. obs: 105146 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.68 Å2 / CC1/2: 0.995 / Rsym value: 0.07 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10362 / CC1/2: 0.805 / Rsym value: 0.445 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.65→28.71 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.9861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1934 10203 4.98 %
Rwork0.163 194499 -
obs0.1645 204702 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.37 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7464 0 9 735 8208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01447708
X-RAY DIFFRACTIONf_angle_d1.229810473
X-RAY DIFFRACTIONf_chiral_restr0.08081116
X-RAY DIFFRACTIONf_plane_restr0.01391326
X-RAY DIFFRACTIONf_dihedral_angle_d7.51291004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.27373540.25666363X-RAY DIFFRACTION96.25
1.67-1.690.25763440.24746511X-RAY DIFFRACTION95.74
1.69-1.710.26032730.23976487X-RAY DIFFRACTION95.04
1.71-1.730.29833320.22836510X-RAY DIFFRACTION98.29
1.73-1.750.28433930.22066498X-RAY DIFFRACTION97.06
1.75-1.780.23783900.21086460X-RAY DIFFRACTION95.22
1.78-1.80.26793180.20736449X-RAY DIFFRACTION97.07
1.8-1.830.23763850.19826451X-RAY DIFFRACTION97.56
1.83-1.860.21893330.1896539X-RAY DIFFRACTION96.56
1.86-1.890.1993410.18116509X-RAY DIFFRACTION96.26
1.89-1.920.25233090.18076549X-RAY DIFFRACTION97.73
1.92-1.960.23163560.16996474X-RAY DIFFRACTION96.32
1.96-1.990.20033280.17036423X-RAY DIFFRACTION95.75
1.99-2.030.21043480.16396246X-RAY DIFFRACTION94.09
2.03-2.080.2083510.16936348X-RAY DIFFRACTION92.98
2.08-2.130.21143400.16026441X-RAY DIFFRACTION98.25
2.13-2.180.18783450.15936603X-RAY DIFFRACTION97.54
2.18-2.240.20583740.15926360X-RAY DIFFRACTION94.85
2.24-2.310.20072910.15746304X-RAY DIFFRACTION93.67
2.31-2.380.20233280.15476587X-RAY DIFFRACTION97.82
2.38-2.460.18853780.16716589X-RAY DIFFRACTION98.47
2.46-2.560.2173470.15926527X-RAY DIFFRACTION98.07
2.56-2.680.2223020.16176703X-RAY DIFFRACTION97.92
2.68-2.820.19863170.15376583X-RAY DIFFRACTION98.61
2.82-30.19133620.15676543X-RAY DIFFRACTION97.98
3-3.230.16433040.14956665X-RAY DIFFRACTION98.56
3.23-3.550.16222840.1456568X-RAY DIFFRACTION96.75
3.55-4.070.16823660.14186301X-RAY DIFFRACTION94.03
4.07-5.120.12793360.12496330X-RAY DIFFRACTION94.42
5.12-28.710.19593740.18566578X-RAY DIFFRACTION98.33

+
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