[English] 日本語
Yorodumi
- PDB-9bxy: CRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN CO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bxy
TitleCRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH DL-III-117
ComponentsHIV-1 LM/HS clade A/E CRF01 gp120 core
KeywordsVIRAL PROTEIN / HIV-1 GP120 / CLADE A/E CF01
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
: / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsTolbert, W.D. / Niu, L. / Pazgier, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI174908 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI162242 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Optimization of a Piperidine CD4-Mimetic Scaffold Sensitizing HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity.
Authors: Lee, D. / Niu, L. / Ding, S. / Zhu, H. / Tolbert, W.D. / Medjahed, H. / Beaudoin-Bussieres, G. / Abrams, C. / Finzi, A. / Pazgier, M. / Smith 3rd, A.B.
History
DepositionMay 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 LM/HS clade A/E CRF01 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22012
Polymers39,4531
Non-polymers2,76711
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.467, 67.686, 87.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HIV-1 LM/HS clade A/E CRF01 gp120 core


Mass: 39452.723 Da / Num. of mol.: 1 / Mutation: H61Y, Q105H, V108I, H375S, N474D, I475M, K476R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell line (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#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.: 9
Source method: isolated from a genetically manipulated source
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-A1ATE / (3S,5R)-1-[4-(1-carbamimidoyl-L-prolyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)piperidine-3-carboxamide


Mass: 538.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33ClFN7O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 3350 5% PEG 400 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 18, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18965 / % possible obs: 82.4 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Net I/σ(I): 24.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 944 / CC1/2: 0.5 / Rpim(I) all: 0.57 / % possible all: 84.2

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→36.71 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 934 4.93 %
Rwork0.1959 --
obs0.1985 18941 81.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 178 60 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092913
X-RAY DIFFRACTIONf_angle_d1.2063956
X-RAY DIFFRACTIONf_dihedral_angle_d11.88431
X-RAY DIFFRACTIONf_chiral_restr0.062464
X-RAY DIFFRACTIONf_plane_restr0.008495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.230.37191190.32762459X-RAY DIFFRACTION80
2.23-2.360.35811410.28252623X-RAY DIFFRACTION85
2.37-2.550.33871670.26842505X-RAY DIFFRACTION82
2.55-2.80.27721310.2382621X-RAY DIFFRACTION84
2.8-3.210.25541080.21572666X-RAY DIFFRACTION84
3.21-4.040.25811440.18052590X-RAY DIFFRACTION82
4.04-36.710.19621240.15742543X-RAY DIFFRACTION76

+
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