[English] 日本語
Yorodumi
- PDB-6mtr: Crystal structure of VRC43.01 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mtr
TitleCrystal structure of VRC43.01 Fab
Components
  • Antibody VRC43.01 Fab heavy chain
  • Antibody VRC43.01 Fab light chain
KeywordsIMMUNE SYSTEM / Anti-HIV-1 human antibody / MPER / gp41
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsKwon, Y.D. / Druz, A. / Law, W.H. / Peng, D. / Zhang, B. / Doria-Rose, N.A. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: Immunity / Year: 2019
Title: Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual.
Authors: Krebs, S.J. / Kwon, Y.D. / Schramm, C.A. / Law, W.H. / Donofrio, G. / Zhou, K.H. / Gift, S. / Dussupt, V. / Georgiev, I.S. / Schatzle, S. / McDaniel, J.R. / Lai, Y.T. / Sastry, M. / Zhang, B. ...Authors: Krebs, S.J. / Kwon, Y.D. / Schramm, C.A. / Law, W.H. / Donofrio, G. / Zhou, K.H. / Gift, S. / Dussupt, V. / Georgiev, I.S. / Schatzle, S. / McDaniel, J.R. / Lai, Y.T. / Sastry, M. / Zhang, B. / Jarosinski, M.C. / Ransier, A. / Chenine, A.L. / Asokan, M. / Bailer, R.T. / Bose, M. / Cagigi, A. / Cale, E.M. / Chuang, G.Y. / Darko, S. / Driscoll, J.I. / Druz, A. / Gorman, J. / Laboune, F. / Louder, M.K. / McKee, K. / Mendez, L. / Moody, M.A. / O'Sullivan, A.M. / Owen, C. / Peng, D. / Rawi, R. / Sanders-Buell, E. / Shen, C.H. / Shiakolas, A.R. / Stephens, T. / Tsybovsky, Y. / Tucker, C. / Verardi, R. / Wang, K. / Zhou, J. / Zhou, T. / Georgiou, G. / Alam, S.M. / Haynes, B.F. / Rolland, M. / Matyas, G.R. / Polonis, V.R. / McDermott, A.B. / Douek, D.C. / Shapiro, L. / Tovanabutra, S. / Michael, N.L. / Mascola, J.R. / Robb, M.L. / Kwong, P.D. / Doria-Rose, N.A.
History
DepositionOct 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 3, 2024Group: 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Antibody VRC43.01 Fab heavy chain
L: Antibody VRC43.01 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,2592
Polymers47,2592
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-27 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.075, 54.661, 66.113
Angle α, β, γ (deg.)90.00, 113.30, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody Antibody VRC43.01 Fab heavy chain


Mass: 24478.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Antibody VRC43.01 Fab light chain


Mass: 22780.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 34% PEG 4000, 0.2M Ammonium Acetate, 0.1M Na Citrate 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 42070 / % possible obs: 84.8 % / Redundancy: 3.7 % / CC1/2: 0.883 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.067 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.733 / Num. unique all: 1715 / CC1/2: 0.556 / Rpim(I) all: 0.44

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model of VRC43.01

Resolution: 1.798→36.863 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.49
RfactorNum. reflection% reflection
Rfree0.2434 2016 4.81 %
Rwork0.2091 --
obs0.2108 41910 83.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→36.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 0 147 3340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113282
X-RAY DIFFRACTIONf_angle_d1.2234504
X-RAY DIFFRACTIONf_dihedral_angle_d11.331926
X-RAY DIFFRACTIONf_chiral_restr0.077521
X-RAY DIFFRACTIONf_plane_restr0.008569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7985-1.84350.3791010.29272145X-RAY DIFFRACTION63
1.8435-1.89330.31131260.28572418X-RAY DIFFRACTION72
1.8933-1.9490.32571280.28272516X-RAY DIFFRACTION74
1.949-2.01190.32411380.26252593X-RAY DIFFRACTION77
2.0119-2.08380.28031320.25682625X-RAY DIFFRACTION78
2.0838-2.16720.28051440.23762711X-RAY DIFFRACTION80
2.1672-2.26590.25271330.22962755X-RAY DIFFRACTION81
2.2659-2.38530.29091460.23992877X-RAY DIFFRACTION85
2.3853-2.53470.28871580.25033168X-RAY DIFFRACTION94
2.5347-2.73040.26391690.24183261X-RAY DIFFRACTION96
2.7304-3.0050.25441640.21013321X-RAY DIFFRACTION98
3.005-3.43960.22041630.19463292X-RAY DIFFRACTION96
3.4396-4.33240.20041580.17983229X-RAY DIFFRACTION94
4.3324-36.87090.23781560.1972983X-RAY DIFFRACTION85
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)
16.89210.72951.04844.81770.69614.35540.1383-0.1975-0.35670.0012-0.08170.2464-0.0625-0.409-0.06490.42230.0052-0.09530.28660.00950.2352-46.317233.5335132.4911
27.279-1.40082.4562.8385-1.04666.82930.11260.0851-0.26290.08170.00670.03360.1510.2578-0.06470.46860.01950.0180.1664-0.02780.2384-15.06911.6717144.705
37.69111.4762.56962.61320.46721.242-0.28730.23150.3831-0.19960.2237-0.0021-0.19830.15110.13420.56-0.0207-0.02510.27550.01190.2656-29.97147.1902132.7613
42.4969-1.887-1.09626.93662.10184.35590.16260.20570.22770.0827-0.1369-0.38670.0428-0.0443-0.01540.48450.03040.05910.30780.02450.2944-11.302421.4121131.765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 2:114 )H2 - 114
2X-RAY DIFFRACTION2( CHAIN H AND RESID 130:229 )H130 - 229
3X-RAY DIFFRACTION3( CHAIN L AND RESID 2:108 )L2 - 108
4X-RAY DIFFRACTION4( CHAIN L AND RESID 109:211 )L109 - 211

+
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://pdbjlvh1.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