[English] 日本語
Yorodumi
- PDB-7rsz: HIV-1 gp120 complex with CJF-II-204 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rsz
TitleHIV-1 gp120 complex with CJF-II-204
ComponentsHIV-1 gp120 Clade C1086
KeywordsVIRAL PROTEIN / HIV-1 gp120 / inhibitor
Function / homologyChem-7IT / Chem-7IW
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsLiang, S. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM116799 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Identification of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.
Authors: Fritschi, C.J. / Liang, S. / Mohammadi, M. / Anang, S. / Moraca, F. / Chen, J. / Madani, N. / Sodroski, J.G. / Abrams, C.F. / Hendrickson, W.A. / Smith 3rd, A.B.
History
DepositionAug 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: HIV-1 gp120 Clade C1086
A: HIV-1 gp120 Clade C1086
C: HIV-1 gp120 Clade C1086
D: HIV-1 gp120 Clade C1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,28737
Polymers161,4774
Non-polymers9,81033
Water86548
1
B: HIV-1 gp120 Clade C1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7679
Polymers40,3691
Non-polymers2,3978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: HIV-1 gp120 Clade C1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,98810
Polymers40,3691
Non-polymers2,6189
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HIV-1 gp120 Clade C1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7679
Polymers40,3691
Non-polymers2,3978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HIV-1 gp120 Clade C1086
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7679
Polymers40,3691
Non-polymers2,3978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.049, 120.775, 195.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
HIV-1 gp120 Clade C1086


Mass: 40369.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#2: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-7IW / N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3R)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide


Mass: 535.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H32ClFN6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-7IT / N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3S)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide


Mass: 535.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H32ClFN6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% PEG 1500 (w/v), 0.1 M CaCl2, 0.1 M imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.79→48.9 Å / Num. obs: 43101 / % possible obs: 99.9 % / Redundancy: 6.25 % / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Net I/σ(I): 12.5
Reflection shellResolution: 2.8→2.91 Å / Num. unique obs: 4401 / CC1/2: 0.457

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGR

3tgr


Resolution: 2.79→48.89 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 2157 5 %
Rwork0.2357 40944 -
obs0.2369 43101 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.04 Å2 / Biso mean: 63.2202 Å2 / Biso min: 16.33 Å2
Refinement stepCycle: final / Resolution: 2.79→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 646 48 11202
Biso mean--71.19 46.29 -
Num. residues----1340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.860.36081290.34422537266694
2.86-2.930.35831200.310727192839100
2.93-3.010.35141400.301627182858100
3.01-3.090.31351390.285326862825100
3.09-3.190.30381680.273126812849100
3.19-3.310.31741430.266327102853100
3.31-3.440.31871180.268627562874100
3.44-3.60.28491440.245627042848100
3.6-3.790.28641400.233827352875100
3.79-4.020.27671370.233627302867100
4.02-4.330.24061500.217827252875100
4.33-4.770.22091480.191327602908100
4.77-5.460.21991570.196227662923100
5.46-6.880.25381470.237127892936100
6.88-48.890.20921770.224429283105100
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)
11.16880.9047-0.22852.1542-1.47531.91680.2446-0.38410.29040.2354-0.0953-0.4383-0.50530.65370.00140.5045-0.0641-0.11530.525-0.03130.52337.509315.4025-13.5518
21.61970.8685-0.53960.96261.11650.32360.326-0.15410.04590.1062-0.4346-0.35190.02130.214500.5960.0505-0.00190.3910.01440.3657-12.488910.567-7.1652
31.2704-0.5955-0.68781.94090.63252.35480.14730.49790.0202-0.3837-0.0068-0.264-0.34110.3071-0.00070.4629-0.01060.00280.47690.01260.4391.718412.3325-29.8102
42.33160.294-0.21761.7417-1.09882.1444-0.05430.3848-0.1603-0.2019-0.08430.09820.2745-0.433400.4460.0462-0.05730.531-0.0480.3895-11.62366.3753-35.3793
51.3288-0.3024-1.16870.35780.45811.04010.0220.116-0.1068-0.01210.15120.1426-0.4253-0.71920.01660.49120.0693-0.00210.4833-0.01190.387-17.54259.2442-17.5642
62.26810.0329-0.5586-0.04140.09321.1125-0.0470.44650.29450.08430.0913-0.1682-0.28940.2410.01330.38930.0376-0.04090.3862-0.01710.37290.61737.2798-27.2818
71.3543-0.1060.3010.0907-1.4030.90870.53530.5283-0.062-0.0382-0.1868-0.71430.41930.7060.02010.73230.08330.13630.5647-0.05340.66283.3774-20.520112.0209
80.02010.8940.19511.87530.2820.7880.49930.0484-0.1583-0.2417-0.2404-0.24850.16960.10350.01440.4833-0.05590.09720.4718-0.07030.57837.7842-8.591520.9991
91.6998-0.59371.01260.61890.50641.2405-0.20230.4664-0.0904-0.6089-0.1057-0.3590.07550.0834-0.00950.5365-0.00570.00920.45730.01260.3698-13.9288-8.86459.9672
101.22810.33190.0811.7765-0.22312.2278-0.0449-0.2662-0.14360.11460.0898-0.33380.16190.17720.00040.38470.00240.02380.3734-0.01880.46342.1019-12.374229.7578
110.17630.6109-0.32980.7359-0.64941.14520.1356-0.6972-0.43740.39820.0368-0.06010.3901-0.30980.00150.460.1080.00950.7816-0.0620.4709-9.5325-12.780942.5564
122.0582-0.42160.54052.9073-1.65022.3974-0.1194-0.49360.12230.14310.09420.0014-0.1774-0.6108-0.01760.39560.02450.05340.5218-0.01450.328-15.7154-6.741332.0906
131.51980.50311.02750.08470.46592.64810.0276-0.4263-0.1315-0.0598-0.0248-0.0841-0.2482-0.02400.3721-0.02650.00540.3468-0.00170.4934-1.5334-6.748430.9383
141.8399-0.5598-0.66631.06710.95481.09150.0687-0.4695-0.49810.4784-0.03330.29870.493-0.3867-00.5901-0.08860.04850.57330.14870.5761-47.7376-18.2166-4.0006
151.78620.430.36080.9584-0.34341.1392-0.0123-0.5212-0.17850.16550.00010.21560.1307-0.3648-00.38830.01260.03770.44110.02340.5397-44.6163-16.2946-8.8595
162.0247-0.670.69582.0133-0.52843.3215-0.01780.6168-0.3764-0.29220.06760.14290.2687-0.125600.4061-0.03910.02630.4835-0.09690.5048-38.0873-17.7991-28.2741
171.28212.1174-0.3382.49920.43290.59-0.15530.2843-0.12910.16640.179-0.1920.07030.1951-0.05210.39670.06590.00320.4903-0.04170.4145-25.6705-12.3576-19.0246
182.3844-0.22840.53021.2941.12391.9669-0.04360.3174-0.23670.0791-0.08970.0670.0335-0.3555-0.00010.4005-0.03090.01760.452-0.00290.5613-45.2205-14.8493-20.4788
191.41631.12510.74810.9711-0.26360.62970.15350.37840.1624-0.3583-0.02550.192-0.1762-0.109600.77620.04510.01510.62240.04920.6531-50.108518.01457.1789
202.7275-0.3401-0.56021.526-0.94983.3086-0.09540.09590.0573-0.1460.19650.2736-0.0621-0.105400.5532-0.068-0.07560.3642-0.00340.4589-43.377114.48659.9866
210.70980.4764-0.83490.10580.06280.26760.08410.4167-0.0635-0.06790.11080.49010.0063-0.495400.55860.05240.00120.60280.02790.7354-54.940920.02816.173
223.4076-0.3004-0.71781.79980.3883.96150.1789-0.84630.33850.1381-0.04670.1138-0.32320.28420.01260.483-0.15350.04070.5844-0.15080.4786-39.670918.621631.8799
231.8925-0.0518-0.546-0.62150.15811.97560.2588-0.30760.4039-0.21090.0210.2485-0.42540.33290.00080.5685-0.06540.08750.3437-0.05170.4858-32.582713.357219.0238
240.7835-0.1010.29110.36790.05650.2240.0049-0.46710.19850.11880.13610.30280.0091-0.7074-00.6022-0.0447-0.00030.78910.01740.6183-50.754612.543923.0573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 49 through 115 )B49 - 115
2X-RAY DIFFRACTION2chain 'B' and (resid 116 through 215 )B116 - 215
3X-RAY DIFFRACTION3chain 'B' and (resid 216 through 352 )B216 - 352
4X-RAY DIFFRACTION4chain 'B' and (resid 353 through 412 )B353 - 412
5X-RAY DIFFRACTION5chain 'B' and (resid 413 through 442 )B413 - 442
6X-RAY DIFFRACTION6chain 'B' and (resid 443 through 491 )B443 - 491
7X-RAY DIFFRACTION7chain 'A' and (resid 48 through 83 )A48 - 83
8X-RAY DIFFRACTION8chain 'A' and (resid 84 through 115 )A84 - 115
9X-RAY DIFFRACTION9chain 'A' and (resid 116 through 215 )A116 - 215
10X-RAY DIFFRACTION10chain 'A' and (resid 216 through 327 )A216 - 327
11X-RAY DIFFRACTION11chain 'A' and (resid 328 through 352 )A328 - 352
12X-RAY DIFFRACTION12chain 'A' and (resid 353 through 442 )A353 - 442
13X-RAY DIFFRACTION13chain 'A' and (resid 443 through 491 )A443 - 491
14X-RAY DIFFRACTION14chain 'C' and (resid 48 through 115 )C48 - 115
15X-RAY DIFFRACTION15chain 'C' and (resid 116 through 258 )C116 - 258
16X-RAY DIFFRACTION16chain 'C' and (resid 259 through 405 )C259 - 405
17X-RAY DIFFRACTION17chain 'C' and (resid 406 through 442 )C406 - 442
18X-RAY DIFFRACTION18chain 'C' and (resid 443 through 492 )C443 - 492
19X-RAY DIFFRACTION19chain 'D' and (resid 49 through 115 )D49 - 115
20X-RAY DIFFRACTION20chain 'D' and (resid 116 through 235 )D116 - 235
21X-RAY DIFFRACTION21chain 'D' and (resid 236 through 258 )D236 - 258
22X-RAY DIFFRACTION22chain 'D' and (resid 259 through 421 )D259 - 421
23X-RAY DIFFRACTION23chain 'D' and (resid 422 through 456 )D422 - 456
24X-RAY DIFFRACTION24chain 'D' and (resid 457 through 491 )D457 - 491

+
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