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- PDB-1hek: Crystal structure of equine infectious anaemia virus matrix antig... -

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Basic information

Entry
Database: PDB / ID: 1hek
TitleCrystal structure of equine infectious anaemia virus matrix antigen (EIAV MA)
ComponentsGAG POLYPROTEIN, CORE PROTEIN P15
KeywordsVIRAL PROTEIN / MEMBRANE-BINDING SWITCHING
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
Retroviral nucleocapsid Gag protein p24, N-terminal / Gag protein p15 / Gag protein p15 / Immunodeficiency lentiviruses, gag gene matrix protein p17 / : / gag protein p24 N-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / DNA polymerase; domain 1 ...Retroviral nucleocapsid Gag protein p24, N-terminal / Gag protein p15 / Gag protein p15 / Immunodeficiency lentiviruses, gag gene matrix protein p17 / : / gag protein p24 N-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / DNA polymerase; domain 1 / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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
Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesEQUINE INFECTIOUS ANEMIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsHatanaka, H. / Iourin, O. / Rao, Z. / Fry, E. / Kingsman, A. / Stuart, D.I.
CitationJournal: J.Virol. / Year: 2002
Title: Structure of Equine Infectious Anemia Virus Matrix Protein.
Authors: Hatanaka, H. / Iourin, O. / Rao, Z. / Fry, E. / Kingsman, A. / Stuart, D.I.
History
DepositionNov 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAG POLYPROTEIN, CORE PROTEIN P15
B: GAG POLYPROTEIN, CORE PROTEIN P15


Theoretical massNumber of molelcules
Total (without water)30,0452
Polymers30,0452
Non-polymers00
Water00
1
A: GAG POLYPROTEIN, CORE PROTEIN P15


Theoretical massNumber of molelcules
Total (without water)15,0231
Polymers15,0231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GAG POLYPROTEIN, CORE PROTEIN P15


Theoretical massNumber of molelcules
Total (without water)15,0231
Polymers15,0231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.150, 47.150, 204.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.89805, -0.43629, 0.05617), (0.43915, 0.89661, -0.05682), (-0.02558, 0.0757, 0.9968)
Vector: 11.22631, 21.75827, -18.20185)

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Components

#1: Protein GAG POLYPROTEIN, CORE PROTEIN P15 / EIAV MA / MATRIX PROTEIN / P15


Mass: 15022.591 Da / Num. of mol.: 2 / Fragment: MA PROTEIN
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN HAS AN N-TERMINAL EXTENTION OF SEVEN RESIDUES DUE TO THE EXPRESSION CONSTRUCT.
Source: (gene. exp.) EQUINE INFECTIOUS ANEMIA VIRUS / Strain: ISOLATE WYOMING / Gene: GAG / Variant: CLONE P3.2-1 / Plasmid: PET-32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03351, UniProt: P69732*PLUS
Has protein modificationY
Sequence detailsRESIDUES -6 TO 0 ARE A CLONING ARTIFACT

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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: 2.55 Å3/Da / Density % sol: 51.43 % / Description: FIGURES ARE SHOWN FOR THE WAVELENGTH 0.91116.
Crystal growTemperature: 291 K / pH: 6.5
Details: 30% PEG5000, 0.2M AMMONIUM SULFATE, 0.1M MES (PH6.5), 291K, pH 6.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG50001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.5
42.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9116, 0.9781, 0.9778
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97811
30.97781
ReflectionResolution: 2.8→24 Å / Num. obs: 6347 / % possible obs: 99 % / Redundancy: 3 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.6 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 24 Å / % possible obs: 99 % / Num. measured all: 19170
Reflection shell
*PLUS
% possible obs: 99 % / Num. unique obs: 633 / Num. measured obs: 1780 / Rmerge(I) obs: 0.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→23.78 Å / Rfactor Rfree error: 0.014 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUES 110 TO 124 WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.373 671 10.9 %RANDOM
Rwork0.279 ---
obs0.279 6153 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 79.4 Å2
Baniso -1Baniso -2Baniso -3
1-22.08 Å224.47 Å20 Å2
2--22.08 Å20 Å2
3----44.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a1.14 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 2.8→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 0 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
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_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.063
X-RAY DIFFRACTIONc_mcangle_it3.644
X-RAY DIFFRACTIONc_scbond_it2.814
X-RAY DIFFRACTIONc_scangle_it4.55
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.587 115 12.8 %
Rwork0.458 783 -
obs--85.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor obs: 0.458

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