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- PDB-2gol: Xray Structure of Gag278 -

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Basic information

Entry
Database: PDB / ID: 2gol
TitleXray Structure of Gag278
Components
  • Capsid protein p24 (CA)
  • Matrix protein p17 (MA)
KeywordsVIRAL PROTEIN / Viral Maturation / Immature / Gag / HIV-1
Function / homology
Function and homology information


viral process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...viral process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / viral capsid / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral nucleocapsid Gag protein p24, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral nucleocapsid Gag protein p24, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA polymerase; domain 1 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag protein / Gag protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKelly, B.N.
CitationJournal: Biochemistry / Year: 2006
Title: Implications for Viral Capsid Assembly from Crystal Structures of HIV-1 Gag 1-278 and CAN 133-278.
Authors: Kelly, B.N. / Howard, B.R. / Wang, H. / Robinson, H. / Sundquist, W.I. / Hill, C.P.
History
DepositionApr 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE BIOLOGICAL MOLECULE IS ONE MATRIX PROTEIN CONNECTED TO ONE CAPSID PROTEIN. SINCE THERE IS NO ELECTRON DENSITY FOR THE LINKER BETWEEN THE MA DOMAIN AND EITHER CA DOMAIN THE AUTHORS ARE UNABLE TO DETERMINE WHICH CA SHOULD CONNECT TO MA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p17 (MA)
B: Capsid protein p24 (CA)
D: Capsid protein p24 (CA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6055
Polymers47,4133
Non-polymers1922
Water4,936274
1
A: Matrix protein p17 (MA)
B: Capsid protein p24 (CA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3053
Polymers31,2092
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Capsid protein p24 (CA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3012
Polymers16,2051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.027, 111.027, 113.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Matrix protein p17 (MA)


Mass: 15003.958 Da / Num. of mol.: 1 / Fragment: residues 1-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: isolate New York-5 / Gene: GAG / Production host: Escherichia coli (E. coli) / References: UniProt: P12497, UniProt: Q674X2*PLUS
#2: Protein Capsid protein p24 (CA)


Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: N-terminal Domain (residues 132-277)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: isolate New York-5 / Gene: GAG / Production host: Escherichia coli (E. coli) / References: UniProt: P12497, UniProt: Q4JL05*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 28% PEG 8000, 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511
SYNCHROTRONNSLS X12C20.97791
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 2, 2004
ADSC QUANTUM 2102CCDJan 7, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.977911
ReflectionResolution: 2.2→30 Å / Num. obs: 34399 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.26 Å / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→79.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.262 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.187 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25832 1703 5 %RANDOM
Rwork0.20251 ---
obs0.20527 32633 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.438 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2---1.79 Å20 Å2
3---3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 10 274 3219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0213009
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.9414084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.6825369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09124.586133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.41519
X-RAY DIFFRACTIONr_chiral_restr0.1790.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022254
X-RAY DIFFRACTIONr_nbd_refined0.2390.21513
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22097
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.231
X-RAY DIFFRACTIONr_mcbond_it1.5961.51928
X-RAY DIFFRACTIONr_mcangle_it2.58523011
X-RAY DIFFRACTIONr_scbond_it3.55531262
X-RAY DIFFRACTIONr_scangle_it5.4414.51073
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 88 -
Rwork0.254 1834 -
obs--72.12 %

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