[English] 日本語
Yorodumi
- PDB-2qhr: Crystal structure of the 13F6-1-2 Fab fragment bound to its Ebola... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qhr
TitleCrystal structure of the 13F6-1-2 Fab fragment bound to its Ebola virus glycoprotein peptide epitope.
Components
  • 13F6-1-2 Fab fragment V lambda x light chain
  • 13F6-1-2 Fab fragment heavy chain
  • Envelope glycoprotein peptide
KeywordsImmune system/viral protein / immunologlobulin fold / antibody-peptide complex / Immune system-viral protein COMPLEX
Function / homology
Function and homology information


Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade ...Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig lambda-2 chain C region / Envelope glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, J.E. / Kuehne, A. / Abelson, D.M. / Fusco, M.L. / Hart, M.K. / Saphire, E.O.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Complex of a protective antibody with its Ebola virus GP peptide epitope: unusual features of a V lambda x light chain.
Authors: Lee, J.E. / Kuehne, A. / Abelson, D.M. / Fusco, M.L. / Hart, M.K. / Saphire, E.O.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.version
Revision 1.3Aug 30, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999sequence The sequences of 13F6-1-2 Fab fragment heavy chain and light chain did not exist in UNP ...sequence The sequences of 13F6-1-2 Fab fragment heavy chain and light chain did not exist in UNP database at the time of processing. The synthetic Envelope glycoprotein peptide naturally exists in Zaire Ebolavirus as residues 404-414.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: 13F6-1-2 Fab fragment heavy chain
L: 13F6-1-2 Fab fragment V lambda x light chain
P: Envelope glycoprotein peptide


Theoretical massNumber of molelcules
Total (without water)49,0343
Polymers49,0343
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.240, 70.300, 142.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody 13F6-1-2 Fab fragment heavy chain


Mass: 23993.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse)
#2: Antibody 13F6-1-2 Fab fragment V lambda x light chain


Mass: 23629.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01844
#3: Protein/peptide Envelope glycoprotein peptide


Mass: 1410.452 Da / Num. of mol.: 1 / Fragment: Envelope glycoprotein peptide, residues 404-414 / Source method: obtained synthetically
Details: The sequence of the peptide occurs in Ebolavirus (Zaire subtype) Envelope Glycoprotein as residues 404-414.
References: UniProt: P87671*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 295 K
Details: 16% (w/v) PEG 8000, 0.04M potassium phosphate, 20% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.29 Å / Num. obs: 86917 / % possible obs: 99.7 % / Redundancy: 4.02 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.51 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7

-
Phasing

Phasing MRCor.coef. Fo:Fc: 0.433 / Packing: 0.412
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral99.1 0

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
CNSrefinement
d*TREK9.4DDzdata scaling
PDB_EXTRACT2data extraction
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEC

1yec


Resolution: 2→46.29 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4412 5.08 %RANDOM
Rwork0.203 ---
obs-86917 97.4 %-
Solvent computationBsol: 61.7 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-14.205 Å20 Å20 Å2
2--15.006 Å20 Å2
3---15.585 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 233 3659
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d1.346
X-RAY DIFFRACTIONf_dihedral_angle_d11.195
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
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)
11.0746-0.1619-0.83820.58010.20921.2728-0.0699-0.06270.0928-0.01830.00750.0014-0.04770.09790.06240.06990.0079-0.01260.15440.00280.135379.948-13.40572.3127
21.3025-0.28360.3243.3845-1.47331.42340.1567-0.016-0.15020.0909-0.3109-0.20190.00130.05020.15420.17430.0161-0.00470.0591-0.00710.086372.4531-18.8433106.2096
30.84690.3612-0.21341.5867-0.52.0273-0.08580.0499-0.17090.00120.108-0.02010.1044-0.1199-0.02220.0876-0.01640.0090.10460.00020.100675.933-34.001868.891
40.6978-0.5503-0.17182.27220.54111.22650.111-0.00460.047-0.0807-0.18320.3413-0.0055-0.03810.07210.14530.01870.00580.0677-0.02210.142860.5498-29.276104.8207
57.70154.33562.26825.55591.0852.4687-0.27280.85550.1981-0.24430.55160.0212-0.02150.2536-0.27880.1388-0.04590.05370.27560.0320.067883.9361-19.050654.3121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 113
2X-RAY DIFFRACTION2H114 - 212
3X-RAY DIFFRACTION3L2 - 110
4X-RAY DIFFRACTION4L111 - 210
5X-RAY DIFFRACTION5P404 - 414

+
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