[English] 日本語
Yorodumi
- PDB-12qb: Crystal structure of CM11.1 Fab in complex with an orthomarburgvi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 12qb
TitleCrystal structure of CM11.1 Fab in complex with an orthomarburgvirus GP2 peptide
Components
  • CM11.1 Fab heavy chain
  • CM11.1 Fab light chain
  • GP2 peptide
KeywordsIMMUNE SYSTEM / orthomarburgvirus / cross-reactive / antibody / GP2
Function / homology
Function and homology information


fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
TLV/ENV coat polyprotein / Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Orthomarburgvirus marburgense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNiyongabo, A. / Janus, B.M. / Ofek, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Crystal structure of CM11.1 Fab in complex with an orthomarburgvirus GP2 peptide
Authors: Niyongabo, A. / Janus, B.M. / Ofek, G.
History
DepositionApr 14, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: CM11.1 Fab heavy chain
L: CM11.1 Fab light chain
P: GP2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9225
Polymers48,8733
Non-polymers492
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-51 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.311, 75.104, 88.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-438-

HOH

-
Components

#1: Antibody CM11.1 Fab heavy chain


Mass: 23724.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Macaca mulatta (Rhesus monkey)
#2: Antibody CM11.1 Fab light chain


Mass: 22973.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Macaca mulatta (Rhesus monkey)
#3: Protein/peptide GP2 peptide


Mass: 2175.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Orthomarburgvirus marburgense / References: UniProt: Q1PDC7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20%(v/v) PEG 8000, 20%(v/v) PEG 400, 0.1M Magnesium Chloride, 0.1M Tris base/Hydrochloric Acid pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.43 Å / Num. obs: 20558 / % possible obs: 95.7 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 1936

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.43 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.35 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 2001 9.74 %
Rwork0.1759 --
obs0.1804 20554 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 2 200 3543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.052
X-RAY DIFFRACTIONf_dihedral_angle_d12.741215
X-RAY DIFFRACTIONf_chiral_restr0.06524
X-RAY DIFFRACTIONf_plane_restr0.01600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.23411350.16681236X-RAY DIFFRACTION90
2.36-2.420.23531480.16621279X-RAY DIFFRACTION96
2.42-2.490.25621350.15581310X-RAY DIFFRACTION97
2.49-2.580.22891390.16311355X-RAY DIFFRACTION97
2.58-2.670.23861390.16161302X-RAY DIFFRACTION97
2.67-2.770.24251530.171343X-RAY DIFFRACTION98
2.77-2.90.21721430.16871327X-RAY DIFFRACTION97
2.9-3.050.22661370.17141271X-RAY DIFFRACTION94
3.05-3.240.23211480.17471356X-RAY DIFFRACTION98
3.24-3.490.21731480.17351336X-RAY DIFFRACTION98
3.49-3.850.22151420.16491325X-RAY DIFFRACTION96
3.85-4.40.17391390.16171296X-RAY DIFFRACTION92
4.4-5.540.18541380.1751364X-RAY DIFFRACTION96
5.55-44.430.2651570.23781453X-RAY DIFFRACTION97

+
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