[English] 日本語
Yorodumi
- PDB-6avn: Crystal structure of unbound anti-HIV antibody Fab PGV19 at 2.5 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6avn
TitleCrystal structure of unbound anti-HIV antibody Fab PGV19 at 2.5 A
Components
  • PGV19 Fab heavy chain
  • PGV19 Fab light chain
KeywordsIMMUNE SYSTEM / VRC01-class lambda antibody / CD4 binding site epitope / anti-HIV neutralizing antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSarkar, A. / Wilson, I.A.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer.
Authors: Sarkar, A. / Bale, S. / Behrens, A.J. / Kumar, S. / Sharma, S.K. / de Val, N. / Pallesen, J. / Irimia, A. / Diwanji, D.C. / Stanfield, R.L. / Ward, A.B. / Crispin, M. / Wyatt, R.T. / Wilson, I.A.
History
DepositionSep 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: PGV19 Fab heavy chain
L: PGV19 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0737
Polymers46,4662
Non-polymers6075
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-21 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.783, 69.783, 193.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Antibody PGV19 Fab heavy chain


Mass: 24246.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: phCMV3 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody PGV19 Fab light chain


Mass: 22219.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: phCMV3 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 10% (v/v) glycerol, 0.1 M ammonium sulfate, 0.1 M HEPES (pH 7.5), 5% (w/v) PEG 3000 and 30% (v/v) PEG 400

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17498 / % possible obs: 100 % / Redundancy: 7.8 % / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7.8 % / Num. unique obs: 837 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: 000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LSU

4lsu


Resolution: 2.5→49.344 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 867 5 %
Rwork0.1986 --
obs0.2012 17336 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 40 153 3414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023344
X-RAY DIFFRACTIONf_angle_d0.5564539
X-RAY DIFFRACTIONf_dihedral_angle_d11.4881982
X-RAY DIFFRACTIONf_chiral_restr0.044498
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65670.29911400.23422669X-RAY DIFFRACTION100
2.6567-2.86180.30281410.23172671X-RAY DIFFRACTION100
2.8618-3.14970.24321430.21412708X-RAY DIFFRACTION100
3.1497-3.60540.23671430.19472723X-RAY DIFFRACTION100
3.6054-4.54190.23411450.16652760X-RAY DIFFRACTION100
4.5419-49.35360.24141550.20122938X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.3809 Å / Origin y: -5.1523 Å / Origin z: -15.4183 Å
111213212223313233
T0.2672 Å2-0.0099 Å2-0.005 Å2-0.2553 Å2-0.0354 Å2--0.2299 Å2
L1.4527 °2-0.3702 °2-0.3345 °2-0.4683 °20.0321 °2--0.1083 °2
S-0.0167 Å °-0.0467 Å °0.0026 Å °0.0416 Å °0.0219 Å °-0.0693 Å °0.0322 Å °-0.0066 Å °-0.0089 Å °
Refinement TLS groupSelection details: all

+
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