[English] 日本語
Yorodumi
- PDB-9mso: Crystal structure of MPXV A35R in complex with neutralizing antib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mso
TitleCrystal structure of MPXV A35R in complex with neutralizing antibody EV35-6
Components
  • EV35-6 heavy chain
  • EV35-6 light chain
  • Protein OPG161
KeywordsIMMUNE SYSTEM / antibody / mpox / monkeypox / A35
Function / homologyChordopoxvirus A33R / Chordopoxvirus A33R protein / C-type lectin-like/link domain superfamily / host cell membrane / C-type lectin fold / virion membrane / membrane / Protein OPG161
Function and homology information
Biological speciesHomo sapiens (human)
Monkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsYuan, M. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142737 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI168631 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA267776 United States
CitationJournal: Cell / Year: 2025
Title: Human monoclonal antibodies targeting A35 protect from death caused by mpox.
Authors: Fantin, R.F. / Yuan, M. / Park, S.C. / Bozarth, B. / Cohn, H. / Ignacio, M. / Earl, P. / Civljak, A. / Laghlali, G. / Zhang, D. / Zhu, X. / Crandell, J. / Monteiro, V. / Clark, J.J. / ...Authors: Fantin, R.F. / Yuan, M. / Park, S.C. / Bozarth, B. / Cohn, H. / Ignacio, M. / Earl, P. / Civljak, A. / Laghlali, G. / Zhang, D. / Zhu, X. / Crandell, J. / Monteiro, V. / Clark, J.J. / Cotter, C. / Burkhardt, M. / Singh, G. / Warang, P. / Garcia-Bernalt Diego, J. / Srivastava, K. / Lugo, L.A. / Pischel, L. / Yildirim, I. / Omer, S.B. / da Silva, D. / Krammer, F. / Bajic, G. / Simon, V. / Schotsaert, M. / Lucas, C. / Wilson, I.A. / Moss, B. / Coelho, C.H.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: EV35-6 heavy chain
L: EV35-6 light chain
G: Protein OPG161
I: Protein OPG161
A: EV35-6 heavy chain
B: EV35-6 light chain
E: Protein OPG161
F: Protein OPG161


Theoretical massNumber of molelcules
Total (without water)141,1698
Polymers141,1698
Non-polymers00
Water00
1
H: EV35-6 heavy chain
L: EV35-6 light chain
G: Protein OPG161
I: Protein OPG161


Theoretical massNumber of molelcules
Total (without water)70,5854
Polymers70,5854
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: EV35-6 heavy chain
B: EV35-6 light chain
E: Protein OPG161
F: Protein OPG161


Theoretical massNumber of molelcules
Total (without water)70,5854
Polymers70,5854
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.504, 165.497, 118.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody EV35-6 heavy chain


Mass: 24405.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody EV35-6 light chain


Mass: 23350.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein
Protein OPG161


Mass: 11414.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG161, MPXVgp145 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A7H0DND2
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% glycerol, 16% PEG-8000 (v/v), and 0.04 M KH2PO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 23030 / % possible obs: 95.5 % / Redundancy: 5.3 % / CC1/2: 0.853 / CC star: 0.959 / Rmerge(I) obs: 0.393 / Rpim(I) all: 0.186 / Rrim(I) all: 0.437 / Χ2: 0.921 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.25-3.313.71.20810640.3240.70.6631.3871.01488.5
3.31-3.3741.11610660.330.7050.5961.2730.94390.4
3.37-3.434.81.00310550.4280.7740.4971.1260.90391.1
3.43-3.55.10.99310710.6130.8720.4731.1060.94290.2
3.5-3.585.30.83810900.4950.8140.4010.9340.94191.6
3.58-3.665.50.67410890.7070.910.3130.7460.94890.4
3.66-3.755.30.60210940.8190.9490.2810.6680.93994
3.75-3.855.40.55910960.820.9490.2570.6180.91291.7
3.85-3.975.40.5311500.6790.8990.2530.590.99195.9
3.97-4.095.40.47211200.7720.9330.2260.5260.93795.2
4.09-4.245.40.37711550.8860.9690.1810.4210.92396.8
4.24-4.415.20.30311690.9190.9790.1470.3380.95798.2
4.41-4.615.10.26611970.9170.9780.1310.2980.92797.9
4.61-4.854.80.2411850.9270.9810.1220.270.93897.9
4.85-5.165.30.2511860.9260.980.1230.280.95599.3
5.16-5.5660.27512090.9180.9780.1250.3040.94899.8
5.56-6.116.30.34812270.9260.9810.1530.3810.883100
6.11-76.50.42112310.9140.9770.180.4590.9399.8
7-8.816.20.26112450.9630.9910.1130.2850.89199.9
8.81-505.60.11313310.9880.9970.0510.1250.71599

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→43.9 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1131 5.25 %
Rwork0.2403 --
obs0.2408 21533 87.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9073 0 0 0 9073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.492
X-RAY DIFFRACTIONf_dihedral_angle_d11.3843276
X-RAY DIFFRACTIONf_chiral_restr0.041410
X-RAY DIFFRACTIONf_plane_restr0.0041611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.320.3891890.34851509X-RAY DIFFRACTION53
3.32-3.50.32361210.31332411X-RAY DIFFRACTION84
3.5-3.720.30261440.28912476X-RAY DIFFRACTION86
3.72-40.27361370.26382565X-RAY DIFFRACTION88
4-4.410.24871490.22392688X-RAY DIFFRACTION92
4.41-5.040.21541570.21522784X-RAY DIFFRACTION95
5.04-6.350.22641620.22272925X-RAY DIFFRACTION99
6.35-43.90.22091720.21073044X-RAY DIFFRACTION99

+
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