[English] 日本語
Yorodumi
- PDB-5xrq: Crystal structure of human monoclonal antibody H3v-47 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xrq
TitleCrystal structure of human monoclonal antibody H3v-47
Components
  • Fab H3v-47 heavy chain
  • Fab H3v-47 light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / heavy chain / light chain
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsZhang, H. / Willson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
CitationJournal: Nat Commun / Year: 2018
Title: A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA.
Authors: Bangaru, S. / Zhang, H. / Gilchuk, I.M. / Voss, T.G. / Irving, R.P. / Gilchuk, P. / Matta, P. / Zhu, X. / Lang, S. / Nieusma, T. / Richt, J.A. / Albrecht, R.A. / Vanderven, H.A. / Bombardi, ...Authors: Bangaru, S. / Zhang, H. / Gilchuk, I.M. / Voss, T.G. / Irving, R.P. / Gilchuk, P. / Matta, P. / Zhu, X. / Lang, S. / Nieusma, T. / Richt, J.A. / Albrecht, R.A. / Vanderven, H.A. / Bombardi, R. / Kent, S.J. / Ward, A.B. / Wilson, I.A. / Crowe, J.E.
History
DepositionJun 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain
A: Fab H3v-47 heavy chain
B: Fab H3v-47 light chain


Theoretical massNumber of molelcules
Total (without water)96,9684
Polymers96,9684
Non-polymers00
Water1,910106
1
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain


Theoretical massNumber of molelcules
Total (without water)48,4842
Polymers48,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-23 kcal/mol
Surface area19430 Å2
MethodPISA
2
A: Fab H3v-47 heavy chain
B: Fab H3v-47 light chain


Theoretical massNumber of molelcules
Total (without water)48,4842
Polymers48,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-21 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.126, 135.126, 78.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Antibody Fab H3v-47 heavy chain


Mass: 25227.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Production host: Homo sapiens (human) / References: UniProt: Q6N089
#2: Antibody Fab H3v-47 light chain


Mass: 23256.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% (w/v) polyethylene glycol (PEG) 6000, 0.1 M sodium citrate (pH 5.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 50148 / % possible obs: 98.2 % / Redundancy: 3.4 % / CC1/2: 0.891 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.058 / Rsym value: 0.11 / Net I/σ(I): 8.1
Reflection shellResolution: 2.57→2.61 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1 / Num. unique obs: 2143 / CC1/2: 0.891 / Rpim(I) all: 0.256 / % possible all: 83.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→46.92 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.95
RfactorNum. reflection% reflection
Rfree0.2144 2497 5.14 %
Rwork0.1796 --
obs0.1825 48572 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 0 106 6634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016683
X-RAY DIFFRACTIONf_angle_d1.179100
X-RAY DIFFRACTIONf_dihedral_angle_d15.4534025
X-RAY DIFFRACTIONf_chiral_restr0.0551034
X-RAY DIFFRACTIONf_plane_restr0.0091169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6006-2.65050.30891220.27562248X-RAY DIFFRACTION82
2.6505-2.70450.29291360.28692392X-RAY DIFFRACTION89
2.7045-2.76320.29051210.25592540X-RAY DIFFRACTION93
2.7632-2.82740.27861430.25342534X-RAY DIFFRACTION93
2.8274-2.8980.29891420.25572628X-RAY DIFFRACTION94
2.898-2.97620.25431480.24572553X-RAY DIFFRACTION94
2.9762-3.06350.25781280.21922639X-RAY DIFFRACTION95
3.0635-3.16210.27551570.21692561X-RAY DIFFRACTION94
3.1621-3.27480.25891280.21332604X-RAY DIFFRACTION95
3.2748-3.40550.23771380.19422592X-RAY DIFFRACTION95
3.4055-3.55990.21691420.18582626X-RAY DIFFRACTION95
3.5599-3.74680.21771410.17862565X-RAY DIFFRACTION95
3.7468-3.98030.17631510.16222580X-RAY DIFFRACTION94
3.9803-4.28570.16321360.14742569X-RAY DIFFRACTION95
4.2857-4.71340.15161250.13492624X-RAY DIFFRACTION95
4.7134-5.38710.16091170.13362610X-RAY DIFFRACTION96
5.3871-6.75630.20971500.15372581X-RAY DIFFRACTION94
6.7563-22.43040.22751350.17422603X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -38.4348 Å / Origin y: 66.5561 Å / Origin z: -3.1196 Å
111213212223313233
T0.2719 Å2-0.0573 Å20.0006 Å2-0.3282 Å20.0194 Å2--0.2271 Å2
L0.327 °20.1782 °20.1898 °2-0.1777 °20.1488 °2---0.1187 °2
S-0.0549 Å °0.05 Å °0.0032 Å °-0.0051 Å °0.0459 Å °0.0247 Å °-0.153 Å °0.0379 Å °0.0022 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