[English] 日本語
Yorodumi
- PDB-6mnq: Rhesus macaque anti-HIV V3 antibody DH727.2 with gp120 V3 ZAM18 p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mnq
TitleRhesus macaque anti-HIV V3 antibody DH727.2 with gp120 V3 ZAM18 peptide
Components
  • Ab DH727.2 heavy chain Fab fragment
  • Ab DH727.2 light chain
  • Envelope glycoprotein
KeywordsIMMUNE SYSTEM / HIV-1 gp120 V3 antibody
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsNicely, N.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI120801 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1-AI100645 United States
CitationJournal: Nat Commun / Year: 2019
Title: Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations.
Authors: Han, Q. / Jones, J.A. / Nicely, N.I. / Reed, R.K. / Shen, X. / Mansouri, K. / Louder, M. / Trama, A.M. / Alam, S.M. / Edwards, R.J. / Bonsignori, M. / Tomaras, G.D. / Korber, B. / ...Authors: Han, Q. / Jones, J.A. / Nicely, N.I. / Reed, R.K. / Shen, X. / Mansouri, K. / Louder, M. / Trama, A.M. / Alam, S.M. / Edwards, R.J. / Bonsignori, M. / Tomaras, G.D. / Korber, B. / Montefiori, D.C. / Mascola, J.R. / Seaman, M.S. / Haynes, B.F. / Saunders, K.O.
History
DepositionOct 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: Envelope glycoprotein
H: Ab DH727.2 heavy chain Fab fragment
L: Ab DH727.2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0016
Polymers49,8153
Non-polymers1863
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-20 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.511, 95.780, 58.049
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide Envelope glycoprotein


Mass: 2394.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A0A0K0KAD3
#2: Antibody Ab DH727.2 heavy chain Fab fragment


Mass: 23385.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#3: Antibody Ab DH727.2 light chain


Mass: 24034.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 20% PEG 6,000

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41285 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rpim(I) all: 0.067 / Rsym value: 0.113 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2038 / Rpim(I) all: 0.401 / Rsym value: 0.69 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4HCR

4hcr


Resolution: 1.804→28.993 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.53
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1993 4.83 %Random selection
Rwork0.1846 ---
obs0.1865 41254 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.804→28.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 12 257 3612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083441
X-RAY DIFFRACTIONf_angle_d1.2044678
X-RAY DIFFRACTIONf_dihedral_angle_d13.8961234
X-RAY DIFFRACTIONf_chiral_restr0.048538
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8037-1.84880.24881250.20742601X-RAY DIFFRACTION93
1.8488-1.89870.25881570.21082836X-RAY DIFFRACTION100
1.8987-1.95460.24751280.20332823X-RAY DIFFRACTION100
1.9546-2.01770.25971540.20072816X-RAY DIFFRACTION100
2.0177-2.08980.24781330.19772861X-RAY DIFFRACTION100
2.0898-2.17340.2311500.19812811X-RAY DIFFRACTION100
2.1734-2.27230.26951470.19612800X-RAY DIFFRACTION100
2.2723-2.3920.25911360.19622826X-RAY DIFFRACTION100
2.392-2.54180.22561470.21012821X-RAY DIFFRACTION100
2.5418-2.7380.24971420.20772819X-RAY DIFFRACTION99
2.738-3.01320.27321360.2092821X-RAY DIFFRACTION99
3.0132-3.44860.22961510.18472811X-RAY DIFFRACTION99
3.4486-4.34260.17641450.15622819X-RAY DIFFRACTION99
4.3426-28.99670.18051420.15052796X-RAY DIFFRACTION97
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)
12.4536-0.50050.65363.12821.27552.2637-0.05440.17790.0319-0.03710.04130.50810.0705-0.53010.02460.19630.0267-0.02610.18340.00280.19-26.564-0.919-10.5179
21.2129-0.8651-1.49241.08431.51562.49980.0869-0.02920.0918-0.0486-0.0148-0.0273-0.17260.0253-0.09350.17860.0113-0.02570.11360.01770.1479-18.3826-0.5445-8.4328
32.86560.45080.04893.597-0.19762.57050.00820.067-0.3776-0.06250.0624-0.04580.1229-0.0193-0.05790.0960.0138-0.00440.12360.00970.1412-8.4924-22.8331-27.9558
41.3756-0.3197-0.10962.92780.25842.029-0.0588-0.1099-0.0424-0.00970.0147-0.0325-0.0093-0.01690.04820.09890.0016-0.02180.10930.00240.0934-16.1997-14.07428.2021
52.1920.5241-1.96261.6012-1.28522.48490.0615-0.09830.06390.0996-0.089-0.0168-0.0430.4512-0.00320.1383-0.0135-0.01660.190.01370.13314.7095-24.433-19.0261
62.44820.9002-2.79381.3753-1.71733.9821-0.0957-0.1511-0.08480.1047-0.1094-0.15620.07610.44170.23160.1438-0.0073-0.02490.23610.02440.14485.7776-25.6964-19.2772
71.8389-2.816-1.10749.76921.19217.405-0.1927-0.7465-0.98280.7110.30650.5680.6531-0.4685-0.15090.40020.01470.04590.40820.03840.384-30.5446-0.930611.9778
88.46970.45742.68556.4792-0.69970.98330.311-0.55680.20440.4364-0.02850.2284-0.10.0755-0.29810.42490.06820.03920.4918-0.02740.3068-29.68944.757412.4457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:31)
2X-RAY DIFFRACTION2(chain H and resid 32:124)
3X-RAY DIFFRACTION3(chain H and resid 125:214)
4X-RAY DIFFRACTION4(chain L and resid 1:105)
5X-RAY DIFFRACTION5(chain L and resid 106:160)
6X-RAY DIFFRACTION6(chain L and resid 161:213)
7X-RAY DIFFRACTION7(chain P and resid 305:312)
8X-RAY DIFFRACTION8(chain P and resid 313:318)

+
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