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- PDB-2eia: X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) ... -

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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 / nucleic acid binding / structural constituent of virion / 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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal ...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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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

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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: 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

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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

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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

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