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- PDB-1afv: HIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3 -

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Basic information

Entry
Database: PDB / ID: 1afv
TitleHIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3
Components
  • ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN)
  • ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN)
  • HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN
KeywordsViral protein/Immune system / COMPLEX (VIRAL CAPSID-IMMUNOGLOBULIN) / HIV / CAPSID PROTEIN / P24 / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Immunoglobulin V-Type / Reverse transcriptase connection / Reverse transcriptase connection domain / Immunoglobulin V-set domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Immunoglobulin V-Type / Reverse transcriptase connection / Reverse transcriptase connection domain / Immunoglobulin V-set 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. / Immunoglobulin V-set domain / 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. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
LEAD (II) ION / : / Gag-Pol polyprotein / Igh protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR, ANOMALOUS DISPERSION / Resolution: 3.7 Å
AuthorsMomany, C. / Kovari, L.C. / Prongay, A.J. / Keller, W. / Gitti, R.K. / Lee, B.M. / Gorbalenya, A.E. / Tong, L. / Mcclure, J. / Ehrlich, L.S. ...Momany, C. / Kovari, L.C. / Prongay, A.J. / Keller, W. / Gitti, R.K. / Lee, B.M. / Gorbalenya, A.E. / Tong, L. / Mcclure, J. / Ehrlich, L.S. / Summers, M.F. / Carter, C. / Rossmann, M.G.
Citation
#1: Journal: Structure / Year: 1995
Title: The Use of Antibody Fragments for Crystallization and Structure Determinations
Authors: Kovari, L.C. / Momany, C. / Rossmann, M.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Preparation and Crystallization of a Human Immunodeficiency Virus P24-Fab Complex
Authors: Prongay, A.J. / Smith, T.J. / Rossmann, M.G. / Ehrlich, L.S. / Carter, C.A. / Mcclure, J.
#3: Journal: Aids Res.Hum.Retroviruses / Year: 1990
Title: Expression in Escherichia Coli and Purification of Human Immunodeficiency Virus Type 1 Capsid Protein (P24)
Authors: Ehrlich, L.S. / Krausslich, H.G. / Wimmer, E. / Carter, C.A.
History
DepositionMar 14, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN
B: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN
L: ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN)
H: ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN)
M: ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN)
K: ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7328
Polymers128,3186
Non-polymers4142
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.900, 92.300, 149.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9997, -0.0075, 0.0253), (-0.0088, -0.9986, 0.052), (0.0249, -0.0522, -0.9983)-3.5157, 39.3232, 225.84509
2given(0.9999, -0.0027, 0.015), (-0.003, -0.9998, 0.0189), (0.015, -0.0189, -0.9997)-2.4694, 43.3764, 225.5939
3given(1, -0.0022, 0.0006), (-0.0022, -0.9998, 0.0219), (0.0006, -0.0219, -0.9998)-0.1811, 42.9019, 226.543

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Components

#1: Protein HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN / HIV-1 CA / HIV CA / HIV P24 / P24


Mass: 16716.189 Da / Num. of mol.: 2 / Fragment: AMINO-TERMINAL DOMAIN RESIDUES 1 - 151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: C-12 / Description: IIIB/LAI ISOLATE OF HIV-1; / Cell line: BL21 / Gene: GAG / Plasmid: PHIV-FSII / Species (production host): Escherichia coli / Gene (production host): GAG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497
#2: Antibody ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN) / FAB / FAB LIGHT CHAIN / FAB HEAVY CHAIN


Mass: 23741.270 Da / Num. of mol.: 2
Fragment: LIGHT CHAIN RESIDUES 1 - 217, HEAVY CHAIN RESIDUES 1 - 220
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: BL21 / References: GenBank: 600718
#3: Antibody ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN) / FAB / FAB LIGHT CHAIN / FAB HEAVY CHAIN


Mass: 23701.412 Da / Num. of mol.: 2
Fragment: LIGHT CHAIN RESIDUES 1 - 217, HEAVY CHAIN RESIDUES 1 - 220
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: BL21 / References: UniProt: Q99LC4
#4: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pb

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 7
Details: 16% PEG 3350, 50 MM BISTRIS-HCL, PH 7.0, 0.1% BETA-OCTYLGLUCOSIDE, 1 MM NAN3
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 7.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropCaCl2
212-24 %PEG33501reservoir
340 mMBis tris Cl1reservoir
420 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.909
DetectorType: PRINCETON 2K / Detector: CCD / Date: Dec 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 29703 / % possible obs: 87.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.37 / % possible all: 50.4
Reflection shell
*PLUS
% possible obs: 50.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR, ANOMALOUS DISPERSION
Starting model: FAB

Resolution: 3.7→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE CARBOXY-TERMINAL RESIDUES 152 - 231 OF THE HIV-1 CAPSID PROTEIN ARE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.324 -10 %RANDOM
Rwork0.217 ---
obs0.217 29703 --
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 3.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11054 0 2 0 11056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.589
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.233
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.233

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