[English] 日本語
Yorodumi
- PDB-7rpu: Crystal Structure of Protective Human Antibody 3A6 Fab Against Eb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rpu
TitleCrystal Structure of Protective Human Antibody 3A6 Fab Against Ebola Virus with GP Stalk/MPER Epitope Peptide
Components
  • 3A6 Fab heavy chain
  • 3A6 Fab light chain
  • GP2 epitope peptide
KeywordsANTIVIRAL PROTEIN / Antibody
Function / homology
Function and homology information


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
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Zaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsSalie, Z.L. / Saphire, E.O. / Davis, C.W. / Ahmed, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: To Be Published
Title: Protection against Ebola virus disease and neutralization mechanism of a survivor's anti-stalk-MPER antibody
Authors: Salie, Z.L. / Saphire, E.O.
History
DepositionAug 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3A6 Fab heavy chain
B: 3A6 Fab light chain
P: GP2 epitope peptide


Theoretical massNumber of molelcules
Total (without water)48,7603
Polymers48,7603
Non-polymers00
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-32 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.293, 66.427, 67.981
Angle α, β, γ (deg.)90.000, 104.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody 3A6 Fab heavy chain


Mass: 23047.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 3A6 Fab light chain


Mass: 23996.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide GP2 epitope peptide


Mass: 1714.870 Da / Num. of mol.: 1 / Fragment: residues 626-640 / Source method: obtained synthetically / Source: (synth.) Zaire ebolavirus (strain Eckron-76) / References: UniProt: P87671
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG 3000, 0.1 M Tris, pH 7.0, and 0.2 M sodium chloride

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.27→65.89 Å / Num. obs: 111264 / % possible obs: 93.92 % / Redundancy: 2 % / Biso Wilson estimate: 14.83 Å2 / CC1/2: 0.999 / Net I/σ(I): 11
Reflection shellResolution: 1.27→1.32 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 3378 / CC1/2: 0.88

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS model

Resolution: 1.27→46.78 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.0089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1598 5591 5.03 %
Rwork0.1412 105639 -
obs0.1422 111230 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 1.27→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 0 629 3972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813508
X-RAY DIFFRACTIONf_angle_d1.02754782
X-RAY DIFFRACTIONf_chiral_restr0.0858537
X-RAY DIFFRACTIONf_plane_restr0.0065620
X-RAY DIFFRACTIONf_dihedral_angle_d16.90151279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.290.26371150.22522086X-RAY DIFFRACTION56.16
1.29-1.30.24381230.21372271X-RAY DIFFRACTION60.64
1.3-1.320.24821390.192419X-RAY DIFFRACTION65.56
1.32-1.330.19311490.16752670X-RAY DIFFRACTION71.55
1.33-1.350.22021570.15562983X-RAY DIFFRACTION80.04
1.35-1.370.1821910.14853525X-RAY DIFFRACTION94.84
1.37-1.390.20372340.14223720X-RAY DIFFRACTION99.52
1.39-1.410.16922110.13883743X-RAY DIFFRACTION99.72
1.41-1.430.18191630.13583694X-RAY DIFFRACTION99.84
1.43-1.450.18151910.13473757X-RAY DIFFRACTION99.82
1.45-1.480.15711880.1323738X-RAY DIFFRACTION99.77
1.48-1.510.17271950.12893732X-RAY DIFFRACTION99.75
1.51-1.540.16072060.12243722X-RAY DIFFRACTION99.39
1.54-1.570.15131940.11783682X-RAY DIFFRACTION98.88
1.57-1.60.16961850.11623720X-RAY DIFFRACTION99.92
1.6-1.640.16481850.11733799X-RAY DIFFRACTION99.9
1.64-1.680.15451880.12043698X-RAY DIFFRACTION99.95
1.68-1.720.15522000.12523789X-RAY DIFFRACTION99.87
1.72-1.780.15491930.13373710X-RAY DIFFRACTION99.69
1.78-1.830.16251970.12743717X-RAY DIFFRACTION98.84
1.83-1.90.15682320.1293675X-RAY DIFFRACTION99.62
1.9-1.970.15532050.12673739X-RAY DIFFRACTION99.87
1.97-2.060.12521780.12573790X-RAY DIFFRACTION99.8
2.06-2.170.1422000.12493746X-RAY DIFFRACTION99.7
2.17-2.310.15791910.13633709X-RAY DIFFRACTION99.14
2.31-2.490.15922310.14143703X-RAY DIFFRACTION98.87
2.49-2.740.16821900.14793759X-RAY DIFFRACTION99.57
2.74-3.130.15791760.15843776X-RAY DIFFRACTION99.3
3.13-3.950.1551840.14483738X-RAY DIFFRACTION98.39
3.95-46.780.15742000.15753829X-RAY DIFFRACTION98.94

+
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