[English] 日本語
Yorodumi
- PDB-6v4r: Crystal structure of a chimeric MR78-like antibody chimera-1 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v4r
TitleCrystal structure of a chimeric MR78-like antibody chimera-1 Fab
Components
  • Chimera-1 Fab heavy chain
  • Chimera-1 Fab light chain
KeywordsIMMUNE SYSTEM / Marburg Virus / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.48 Å
AuthorsBozhanova, N.G. / Crowe, J.E. / Meiler, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI141661 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI21799 Ebola United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Discovery of Marburg virus neutralizing antibodies from virus-naive human antibody repertoires using large-scale structural predictions.
Authors: Bozhanova, N.G. / Sangha, A.K. / Sevy, A.M. / Gilchuk, P. / Huang, K. / Nargi, R.S. / Reidy, J.X. / Trivette, A. / Carnahan, R.H. / Bukreyev, A. / Crowe Jr., J.E. / Meiler, J.
History
DepositionNov 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Chimera-1 Fab heavy chain
L: Chimera-1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4952
Polymers47,4952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-24 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.780, 133.780, 91.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Antibody Chimera-1 Fab heavy chain


Mass: 23967.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#2: Antibody Chimera-1 Fab light chain


Mass: 23527.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): Expi293F
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.39 % / Mosaicity: 0.284 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4.5 M NaCl, 0.1 M HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.48→57.93 Å / Num. obs: 12393 / % possible obs: 99.2 % / Redundancy: 16.6 % / Biso Wilson estimate: 145.12 Å2 / Rpim(I) all: 0.084 / Rrim(I) all: 0.342 / Net I/σ(I): 8.8 / Num. measured all: 206074
Reflection shellResolution: 3.48→3.54 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 618 / Rpim(I) all: 0.995 / Rrim(I) all: 4.159 / % possible all: 98.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.563
Highest resolutionLowest resolution
Rotation57.93 Å3.99 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
PHENIXRosetta-Phenixrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRP

5jrp


Resolution: 3.48→57.93 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.608
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3273 524 4.2 %RANDOM
Rwork0.2946 ---
obs0.2961 11852 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 284.51 Å2 / Biso mean: 172.603 Å2 / Biso min: 107.51 Å2
Baniso -1Baniso -2Baniso -3
1-6.54 Å23.27 Å20 Å2
2--6.54 Å2-0 Å2
3----21.21 Å2
Refinement stepCycle: final / Resolution: 3.48→57.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 0 0 3259
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0133342
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172963
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.6434556
X-RAY DIFFRACTIONr_angle_other_deg2.4331.5686940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.185427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54624.091132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.52715525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.47157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023720
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02657
X-RAY DIFFRACTIONr_mcbond_it14.15618.6521717
X-RAY DIFFRACTIONr_mcbond_other14.16318.651715
X-RAY DIFFRACTIONr_mcangle_it19.23927.972141
LS refinement shellResolution: 3.48→3.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 27 -
Rwork0.485 863 -
all-890 -
obs--98.67 %

+
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