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- PDB-1eia: X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) ... -

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Basic information

Entry
Database: PDB / ID: 1eia
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 / TREAT MAD AS MIR / 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 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EIAV CAPSID PROTEIN P26


Theoretical massNumber of molelcules
Total (without water)23,4881
Polymers23,4881
Non-polymers00
Water2,828157
1
A: EIAV CAPSID PROTEIN P26

A: EIAV CAPSID PROTEIN P26

A: EIAV CAPSID PROTEIN P26

A: EIAV CAPSID PROTEIN P26


Theoretical massNumber of molelcules
Total (without water)93,9514
Polymers93,9514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation38_555-y+1/2,-x+1/2,-z+1/21
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation37_545y+1/2,x-1/2,-z+1/21
Unit cell
Length a, b, c (Å)176.760, 176.760, 176.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein EIAV CAPSID PROTEIN P26


Mass: 23487.648 Da / Num. of mol.: 1
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.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.5 / Details: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.72
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 17, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 13201 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 40
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 17 % / Mean I/σ(I) obs: 6 / Rsym value: 0.335 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 48 Å / Num. all: 13201 / Num. obs: 12292
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.357

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PHASESphasing
CNSphasing
RefinementMethod to determine structure: TREAT MAD AS MIR / Resolution: 2.7→48 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1271 10.2 %RANDOM
Rwork0.227 ---
obs0.227 12459 93.8 %-
Displacement parametersBiso mean: 55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 0 1643
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.481.5
X-RAY DIFFRACTIONc_mcangle_it8.722
X-RAY DIFFRACTIONc_scbond_it92
X-RAY DIFFRACTIONc_scangle_it10.852.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 184 10.4 %
Rwork0.335 1589 -
obs--82.5 %
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
Lowest resolution: 48 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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