[English] 日本語
Yorodumi
- PDB-8cta: Minimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cta
TitleMinimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integrase Catalytic Core Domain Dimer and Carboxy Terminal Domains
Components(Integrase) x 2
KeywordsVIRAL PROTEIN / VIRAL DNA INTEGRATION / DNA BINDING / LEDGF BINDING
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
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 ...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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / 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
Similarity search - Domain/homology
Chem-L3D / POL polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsGupta, K. / Van Duyne, G.D. / Eilers, G. / Bushman, F.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 AI 052845 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 angstrom resolution: Routes to inhibitor optimization.
Authors: Eilers, G. / Gupta, K. / Allen, A. / Montermoso, S. / Murali, H. / Sharp, R. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.
History
DepositionMay 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
E: Integrase
F: Integrase
G: Integrase
H: Integrase
I: Integrase
J: Integrase
K: Integrase
L: Integrase
M: Integrase
N: Integrase
O: Integrase
P: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,68251
Polymers190,46616
Non-polymers5,21635
Water1,17165
1
A: Integrase
B: Integrase
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,81211
Polymers47,6174
Non-polymers1,1957
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Integrase
F: Integrase
G: Integrase
H: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,12216
Polymers47,6174
Non-polymers1,50612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Integrase
J: Integrase
K: Integrase
L: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,93613
Polymers47,6174
Non-polymers1,3199
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Integrase
N: Integrase
O: Integrase
P: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,81211
Polymers47,6174
Non-polymers1,1957
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.510, 116.510, 112.800
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Integrase


Mass: 17580.045 Da / Num. of mol.: 8 / Fragment: Catalytic Core Domain / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: pol / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72498
#2: Protein
Integrase


Mass: 6228.216 Da / Num. of mol.: 8 / Fragment: Carboxy Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72498
#3: Chemical
ChemComp-L3D / (2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid


Mass: 442.506 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H26N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20 mM Tris pH 7.4, 250-300 mM NaCl, 1 mM DTT, 25% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.93→19.85 Å / Num. obs: 48717 / % possible obs: 90.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 53.5 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.043 / Rrim(I) all: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 2.93→3.04 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2000 / CC1/2: 0.915 / CC star: 0.999 / Rpim(I) all: 0.59 / Rrim(I) all: 1.25 / % possible all: 41.1

-
Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
PHENIX1.17.1.3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L3U

3l3u


Resolution: 2.93→19.85 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 39.239 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26129 4441 10 %RANDOM
Rwork0.21569 ---
obs0.22023 39969 90.34 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20.12 Å2
2--0.21 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.93→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12031 0 368 65 12464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01712644
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611993
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.81617073
X-RAY DIFFRACTIONr_angle_other_deg0.4731.57227804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3545.2411553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.241102192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1870.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4672.1476017
X-RAY DIFFRACTIONr_mcbond_other3.4672.1476017
X-RAY DIFFRACTIONr_mcangle_it5.5543.2017460
X-RAY DIFFRACTIONr_mcangle_other5.5543.2017461
X-RAY DIFFRACTIONr_scbond_it4.2192.5796627
X-RAY DIFFRACTIONr_scbond_other4.2192.586628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2353.6939614
X-RAY DIFFRACTIONr_long_range_B_refined13.62841.59751334
X-RAY DIFFRACTIONr_long_range_B_other13.62741.59651329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.931→3.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 125 -
Rwork0.352 1123 -
obs--35.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5051-1.1129-1.13094.9519-0.02173.9584-0.08170.0939-0.2512-0.1215-0.0744-1.44110.91260.7840.15620.6282-0.01740.19050.71840.05330.9086-20.268-9.81835.846
24.214-0.3162-1.13523.1335-0.39854.9770.09310.75860.6875-0.7809-0.1978-0.676-0.22520.10960.10470.4033-0.17840.13920.58210.16990.4964-29.7643.8927.717
30.1528-0.6641-0.22043.17031.07580.37580.11620.0497-0.0172-0.0084-0.08620.1640.0071-0.049-0.031.14120.02990.53821.74050.03551.0418-7.943-13.1167.191
49.13430.2824-1.68093.02190.11924.1106-0.3160.392-0.0717-0.37790.25030.6547-0.1794-0.34260.06570.285-0.13080.00570.33630.0370.3835-53.047-6.65945.063
55.5541-0.0681-1.26374.10970.04133.8223-0.0933-0.0445-0.6760.0945-0.0592-0.8910.67350.71670.15250.3176-0.05530.08530.52760.01350.42725.0818.94235.433
65.11480.0515-1.71672.07180.27694.75160.14320.91590.6754-0.6103-0.133-0.2032-0.5351-0.1242-0.01020.3941-0.15260.08540.52030.08810.233915.58132.50226.654
71.4567-1.4762-2.7836.07571.99585.61370.13870.1143-0.08520.0688-0.22360.61590.0793-0.13150.08490.9688-0.06010.34351.4771-0.20070.791135.77713.8356.239
810.8784-1.56730.04873.2753-1.49653.9878-0.23110.1584-0.46290.00110.31541.1387-0.3312-0.462-0.08420.3297-0.07170.05460.40340.02680.4933-7.42922.83845.245
96.2774-1.9048-2.26243.33881.04952.9513-0.2556-0.0119-0.04310.21480.1614-0.68180.52650.61510.09420.2889-0.0479-0.03040.4650.06910.274328.197-41.46338.588
104.7864-0.9305-1.55663.84860.48054.5230.24651.14040.9148-0.7929-0.2332-0.223-0.3223-0.2016-0.01330.3339-0.11480.00250.56030.27550.384318.258-28.14529.162
110.9-1.1999-1.26829.20233.7442.85240.21020.32650.04950.2767-0.4289-0.00660.3348-0.42370.21870.8265-0.03230.29651.35190.30050.48640.422-45.6629.797
129.13730.294-1.71162.92640.04823.5747-0.16390.3753-0.0362-0.2530.12530.819-0.2713-0.11970.03860.2298-0.1354-0.01390.2058-0.01780.4091-5.743-36.9746.166
135.185-1.2015-2.45133.24310.83663.9517-0.233-0.0688-0.26020.33510.1812-0.56780.57720.62430.05170.3128-0.0554-0.01120.4321-0.0130.207873.777-12.35438.251
144.7083-0.7168-1.2493.90490.08663.82250.04351.24491.0975-0.7312-0.08620.1957-0.2183-0.33050.04270.3557-0.1784-0.00710.67760.26150.486863.6170.61428.346
150.1557-0.8841-0.206711.16663.11831.61870.11710.23160.04090.7086-0.28140.71010.6325-0.1340.16430.7613-0.0070.1931.19630.12270.241884.258-18.4688.722
168.6884-0.2054-4.56183.6906-2.19424.4998-0.2970.1215-0.36730.02830.41790.8901-0.3364-0.5098-0.12090.46610.0057-0.03470.3879-0.04560.454640.222-7.63746.71
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 208
2X-RAY DIFFRACTION2B56 - 210
3X-RAY DIFFRACTION3C221 - 271
4X-RAY DIFFRACTION4D222 - 271
5X-RAY DIFFRACTION5E57 - 208
6X-RAY DIFFRACTION6F57 - 210
7X-RAY DIFFRACTION7G221 - 271
8X-RAY DIFFRACTION8H222 - 271
9X-RAY DIFFRACTION9I57 - 208
10X-RAY DIFFRACTION10J57 - 210
11X-RAY DIFFRACTION11K221 - 271
12X-RAY DIFFRACTION12L221 - 271
13X-RAY DIFFRACTION13M56 - 209
14X-RAY DIFFRACTION14N55 - 210
15X-RAY DIFFRACTION15O221 - 271
16X-RAY DIFFRACTION16P220 - 271

+
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://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