[English] 日本語
Yorodumi
- PDB-6xlz: Structure of NHP D11A.F2 Fab in complex with 16055 V2b peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xlz
TitleStructure of NHP D11A.F2 Fab in complex with 16055 V2b peptide
Components
  • Envelope glycoprotein gp160
  • NHP_D11A.F2_Fab_Heavy_chain
  • NHP_D11A.F2_Fab_Light_Chain
KeywordsIMMUNE SYSTEM / Fab / HIV / V1V2 / Complex / Antibody / Scaffold / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAljedani, S. / Rodarte, J. / Liban, T. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI104722 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization.
Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / ...Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / O'Dell, S. / Mascola, J.R. / Lee, K.K. / Karlsson Hedestam, G.B. / Wyatt, R.T. / Pancera, M.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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
P: Envelope glycoprotein gp160
H: NHP_D11A.F2_Fab_Heavy_chain
L: NHP_D11A.F2_Fab_Light_Chain
A: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,92419
Polymers52,5244
Non-polymers1,39915
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-144 kcal/mol
Surface area20370 Å2
Unit cell
Length a, b, c (Å)130.393, 130.393, 170.898
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

-
Components

-
Protein/peptide , 1 types, 2 molecules PA

#1: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 2738.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: A0A0B5KUY7

-
Antibody , 2 types, 2 molecules HL

#2: Antibody NHP_D11A.F2_Fab_Heavy_chain


Mass: 23688.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Antibody NHP_D11A.F2_Fab_Light_Chain


Mass: 23359.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 111 molecules

#4: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0 and 1.32 M K/Na Tartrate at 8.5 mg/ml. Cryo protection: 15% 2R3R Butanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.8→94.22 Å / Num. obs: 21787 / % possible obs: 99.8 % / Redundancy: 22.2 % / Biso Wilson estimate: 52.57 Å2 / CC1/2: 0.72 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 22.2 % / Num. unique obs: 3087 / CC1/2: 0.744 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RFO

4rfo


Resolution: 2.8→94.21 Å / SU ML: 0.2148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 1092 5.03 %
Rwork0.2163 20608 -
obs0.2183 21700 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→94.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 82 96 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983577
X-RAY DIFFRACTIONf_angle_d0.95834888
X-RAY DIFFRACTIONf_chiral_restr0.0523564
X-RAY DIFFRACTIONf_plane_restr0.0063614
X-RAY DIFFRACTIONf_dihedral_angle_d17.43961250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.28381250.2682506X-RAY DIFFRACTION99.1
2.93-3.080.34141420.26172506X-RAY DIFFRACTION99.59
3.08-3.270.27091150.24862539X-RAY DIFFRACTION99.48
3.28-3.530.25221350.21262556X-RAY DIFFRACTION99.96
3.53-3.880.28281320.22462547X-RAY DIFFRACTION99.55
3.88-4.440.23871500.18832547X-RAY DIFFRACTION99.7
4.45-5.60.20721450.17512616X-RAY DIFFRACTION100
5.6-94.210.26081480.23382791X-RAY DIFFRACTION99.9

+
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