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- PDB-1ex4: HIV-1 INTEGRASE CATALYTIC CORE AND C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1ex4
TitleHIV-1 INTEGRASE CATALYTIC CORE AND C-TERMINAL DOMAIN
ComponentsINTEGRASE
KeywordsVIRAL PROTEIN / SH3-like domain / nonspecific DNA binding beta sheet / cis-proline
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / Assembly Of The HIV Virion / exoribonuclease H / exoribonuclease H activity / Budding and maturation of HIV virion / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / 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 / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H-like superfamily/Ribonuclease H / 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 / Ribonuclease H-like superfamily/Ribonuclease H / 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 / SH3 type barrels. / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsChen, J.C.-H. / Krucinski, J. / Miercke, L.J.W. / Finer-Moore, J.S. / Tang, A.H. / Leavitt, A.D. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding.
Authors: Chen, J.C. / Krucinski, J. / Miercke, L.J. / Finer-Moore, J.S. / Tang, A.H. / Leavitt, A.D. / Stroud, R.M.
History
DepositionApr 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3146
Polymers52,8542
Non-polymers2,4604
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-22 kcal/mol
Surface area23760 Å2
MethodPISA
2
A: INTEGRASE
B: INTEGRASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)331,88136
Polymers317,12412
Non-polymers14,75724
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation4_665-y+1,-x+1,-z1
crystal symmetry operation5_555-x+y,y,-z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area56640 Å2
ΔGint-126 kcal/mol
Surface area111640 Å2
MethodPISA
3
A: INTEGRASE
B: INTEGRASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)331,88136
Polymers317,12412
Non-polymers14,75724
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-y,-x,-z1
crystal symmetry operation5_555-x+y,y,-z1
crystal symmetry operation6_555x,x-y,-z1
Buried area41670 Å2
ΔGint-152 kcal/mol
Surface area126610 Å2
MethodPISA
4
A: INTEGRASE
B: INTEGRASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)331,88136
Polymers317,12412
Non-polymers14,75724
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation4_664-y+1,-x+1,-z-11
crystal symmetry operation5_554-x+y,y,-z-11
crystal symmetry operation6_564x,x-y+1,-z-11
Buried area33020 Å2
ΔGint-146 kcal/mol
Surface area135260 Å2
MethodPISA
5
A: INTEGRASE
B: INTEGRASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)331,88136
Polymers317,12412
Non-polymers14,75724
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation4_665-y+1,-x+1,-z1
crystal symmetry operation5_655-x+y+1,y,-z1
crystal symmetry operation6_555x,x-y,-z1
Buried area34110 Å2
ΔGint-132 kcal/mol
Surface area134170 Å2
MethodPISA
6
A: INTEGRASE
B: INTEGRASE
hetero molecules

A: INTEGRASE
B: INTEGRASE
hetero molecules

A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,94118
Polymers158,5626
Non-polymers7,37912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14500 Å2
ΔGint-62 kcal/mol
Surface area69640 Å2
MethodPISA
7
A: INTEGRASE
B: INTEGRASE
hetero molecules

A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62712
Polymers105,7084
Non-polymers4,9198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area12890 Å2
ΔGint-43 kcal/mol
Surface area43200 Å2
MethodPISA
8
A: INTEGRASE
B: INTEGRASE
hetero molecules

A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62712
Polymers105,7084
Non-polymers4,9198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z1
Buried area12280 Å2
ΔGint-47 kcal/mol
Surface area43820 Å2
MethodPISA
9
A: INTEGRASE
B: INTEGRASE
hetero molecules

A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62712
Polymers105,7084
Non-polymers4,9198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area10180 Å2
ΔGint-47 kcal/mol
Surface area45910 Å2
MethodPISA
10
A: INTEGRASE
B: INTEGRASE
hetero molecules

A: INTEGRASE
B: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62712
Polymers105,7084
Non-polymers4,9198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z1
Buried area9750 Å2
ΔGint-40 kcal/mol
Surface area46340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.990, 103.990, 101.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-304-

CPS

21B-303-

CPS

31A-326-

HOH

41B-313-

HOH

Detailsthe biological unit is one homodimer, comprised of chains A and B in the asymmetric unit

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Components

#1: Protein INTEGRASE


Mass: 26427.012 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE AND C-TERMINAL DOMAINS / Mutation: C56S,W131D,F139D,F185K,C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04585
#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: hepes, NaCL, CHAPS, formate, citrate, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 MNa formate1reservoir
2150 mMNa citrate1reservoir
33 mMdithiothreitol1reservoir
43 mMCHAPS1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 15580 / Num. obs: 15580 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.84 / Num. unique all: 782 / % possible all: 100
Reflection
*PLUS
Num. measured all: 178921
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.8→28.26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2275446.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: residues 50-55,142-144, and 271-288 in chain A, residues 50-54,138-149, and 271-288 in chain B, and the side chain of K211 in chain A are disordered and not included in refinement. Water 42 ...Details: residues 50-55,142-144, and 271-288 in chain A, residues 50-54,138-149, and 271-288 in chain B, and the side chain of K211 in chain A are disordered and not included in refinement. Water 42 and CHAPS molecules 301, 302, 303 and 304 are on crystallographic 2-fold axes. Portions of CHAPS molecules 301, 302, and 304 are missing in the electron density. Residues PRO-238 in chains A and B are cis-prolines
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1154 7.4 %RANDOM
Rwork0.258 ---
all0.26 15580 --
obs0.258 15580 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.35 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 72.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.92 Å217.54 Å20 Å2
2--6.92 Å20 Å2
3----13.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 117 79 3450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 185 7.2 %
Rwork0.356 2379 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3chaps_full.prxCHAPS_FULL.TPX
X-RAY DIFFRACTION4chaps_trunc.prxCHAPS_TRUNC.TPX
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_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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