[English] 日本語
Yorodumi
- PDB-2pxr: Crystal Structure of HIV-1 CA146 in the Presence of CAP-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pxr
TitleCrystal Structure of HIV-1 CA146 in the Presence of CAP-1
ComponentsGag-Pol polyprotein (Pr160Gag-Pol)
KeywordsVIRAL PROTEIN / Viral Capsid / HIV-1 / Anti-Viral / Small molecule inhibition
Function / homology
Function and homology information


viral budding via host ESCRT complex / 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 budding via host ESCRT complex / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / host cell cytoplasm / 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 / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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. / 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 polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKelly, B.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Antiviral Assembly Inhibitor CAP-1 Complex with the HIV-1 CA Protein.
Authors: Kelly, B.N. / Kyere, S. / Kinde, I. / Tang, C. / Howard, B.R. / Robinson, H. / Sundquist, W.I. / Summers, M.F. / Hill, C.P.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3714
Polymers16,2051
Non-polymers1663
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules

C: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7428
Polymers32,4092
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2190 Å2
ΔGint-164 kcal/mol
Surface area15420 Å2
MethodPISA
3
C: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules

C: Gag-Pol polyprotein (Pr160Gag-Pol)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7428
Polymers32,4092
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1500 Å2
ΔGint-47 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.187, 62.777, 106.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-400-

CL

21C-402-

ZN

DetailsThe biological assembly is a hexamer

-
Components

#1: Protein Gag-Pol polyprotein (Pr160Gag-Pol)


Mass: 16204.573 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL43 / References: UniProt: P12497, UniProt: Q79791*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH, 5% PEG 8000, 20% PEG 300, 10% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2005
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→53.15 Å / Num. all: 22915 / Num. obs: 21930 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 5.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.2 / Num. measured all: 5356 / Num. unique all: 2570 / Rsym value: 0.318 / % possible all: 78.5

-
Phasing

Phasing MRRfactor: 0.48 / Cor.coef. Fo:Fc: 0.463
Highest resolutionLowest resolution
Rotation3 Å19.64 Å
Translation3 Å19.64 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→53.15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.664 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.102 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Authors also state that The structure 2PXR was determined by X-ray crystallography from crystals of CA146 that were grown in the presence ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Authors also state that The structure 2PXR was determined by X-ray crystallography from crystals of CA146 that were grown in the presence of CAP-1. CAP-1 is not visible in electron density maps, although NMR data provided ligand-protein NOEs that allowed them to build a joint refined structure 2JPR.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1107 5.1 %RANDOM
Rwork0.163 ---
all0.166 22915 --
obs0.166 21916 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.635 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---1.16 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→53.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 3 179 1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211223
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9271666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79225.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83515224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.499157
X-RAY DIFFRACTIONr_chiral_restr0.130.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02925
X-RAY DIFFRACTIONr_nbd_refined0.2390.2618
X-RAY DIFFRACTIONr_nbtor_refined0.310.2864
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0630.23
X-RAY DIFFRACTIONr_mcbond_it2.0241.5764
X-RAY DIFFRACTIONr_mcangle_it2.96121225
X-RAY DIFFRACTIONr_scbond_it3.7573520
X-RAY DIFFRACTIONr_scangle_it5.5444.5441
X-RAY DIFFRACTIONr_rigid_bond_restr2.50631284
X-RAY DIFFRACTIONr_sphericity_free8.6373182
X-RAY DIFFRACTIONr_sphericity_bonded7.00731192
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 63 -
Rwork0.247 1146 -
obs-1209 72.48 %

+
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://pdbjlvh1.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