[English] 日本語
Yorodumi
- PDB-2eia: X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eia
TitleX-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) CAPSID PROTEIN P26
ComponentsEIAV CAPSID PROTEIN P26
KeywordsVIRAL PROTEIN / VIRAL CAPSID EIAV / HIV / LENTIVIRUS
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding
Similarity search - Function
Gag protein p15 / Gag protein p15 / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain ...Gag protein p15 / Gag protein p15 / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEquine infectious anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJin, Z. / Jin, L. / Peterson, D.L. / Lawson, C.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Model for lentivirus capsid core assembly based on crystal dimers of EIAV p26.
Authors: Jin, Z. / Jin, L. / Peterson, D.L. / Lawson, C.L.
#1: Journal: Biochim.Biophys.Acta / Year: 1997
Title: Cloning, Expression, Purification, and Characterization of the Major Core Protein (P26) from Equine Infectious Anemia Virus
Authors: Birkett, A.J. / Yelamos, B. / Rodriguez-Crespo, I. / Gavilanes, F. / Peterson, D.L.
History
DepositionJul 15, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EIAV CAPSID PROTEIN P26
B: EIAV CAPSID PROTEIN P26


Theoretical massNumber of molelcules
Total (without water)46,7732
Polymers46,7732
Non-polymers00
Water3,387188
1
A: EIAV CAPSID PROTEIN P26
B: EIAV CAPSID PROTEIN P26

A: EIAV CAPSID PROTEIN P26
B: EIAV CAPSID PROTEIN P26


Theoretical massNumber of molelcules
Total (without water)93,5464
Polymers93,5464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Unit cell
Length a, b, c (Å)100.480, 100.480, 157.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.544595, 0.821396, -0.169486), (0.71868, 0.352864, -0.599154), (-0.432338, -0.448102, -0.782489)
Vector: -50.91151, 85.34118, 141.24844)
DetailsTHERE ARE TWO MONOMERS IN ONE ASYMMETRIC UNIT AND IN THIS MODEL. THE N-TERMINAL RESIDUES 1-16 AND C-TERMINAL RESIDUES 223-235 WERE NOT SEEN IN THE DENSITY MAPS.

-
Components

#1: Protein EIAV CAPSID PROTEIN P26


Mass: 23386.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine infectious anemia virus / Genus: Lentivirus / Gene: GAG / Gene (production host): GAG / Production host: Escherichia coli (E. coli) / References: UniProt: P69732
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.5
Details: 0.1M SODIUM CITRATE, 10% PEG 3350, 15% ISOPROPANOL, PH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlprotein1drop
21 mMsodium phosphate1drop
30.1 Msodium citrate1reservoir
410 %(w/v)PEG33501reservoir
515 %(v/v)isopropanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0333, 1.07168, 1.07202
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 11, 1997 / Details: MIRROR
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03331
21.071681
31.072021
ReflectionResolution: 2.7→47 Å / Num. obs: 13524 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 20 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12 % / Mean I/σ(I) obs: 3 / Rsym value: 0.283 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 246510 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.326

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3refinement
PHASESphasing
CNS0.3phasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→48 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 274655 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1300 10.3 %RANDOM
Rwork0.236 ---
obs0.236 12647 93.6 %-
Displacement parametersBiso mean: 62.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.36 Å2-10.45 Å20 Å2
2---4.36 Å20 Å2
3---8.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 0 0 3267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 154 8.8 %
Rwork0.336 1606 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor obs: 0.336

+
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