[English] 日本語
Yorodumi
- PDB-8ahn: Sin Nombre virus Gn in complex with Fab SNV-42 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ahn
TitleSin Nombre virus Gn in complex with Fab SNV-42
Components
  • Envelope polyprotein
  • Fab SNV-42 heavy chain
  • Fab SNV-42 light chain
KeywordsVIRAL PROTEIN / Sin Nombre / virus / hantavirus / Fab / SNV-42 / complex
Function / homology
Function and homology information


: / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virion membrane / signal transduction / membrane / metal ion binding
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSin Nombre orthohantavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStass, R. / Bowden, T.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V031635/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2023
Title: Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody.
Authors: Stass, R. / Engdahl, T.B. / Chapman, N.S. / Wolters, R.M. / Handal, L.S. / Diaz, S.M. / Crowe Jr., J.E. / Bowden, T.A.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope polyprotein
L: Fab SNV-42 light chain
H: Fab SNV-42 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4805
Polymers85,8353
Non-polymers6462
Water13,709761
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.926, 146.420, 157.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

-
Components

-
Antibody , 2 types, 2 molecules LH

#2: Antibody Fab SNV-42 light chain


Mass: 22906.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab SNV-42 heavy chain


Mass: 23642.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Protein / Non-polymers , 2 types, 762 molecules A

#1: Protein Envelope polyprotein / M polyprotein


Mass: 39286.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sin Nombre orthohantavirus / Production host: Homo sapiens (human) / References: UniProt: K9MNN9
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 0.2 M tri-ammonium citrate pH 7.0 and 20% w/v polyethylene glycol 3350
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→46.62 Å / Num. obs: 95210 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rrim(I) all: 0.125 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 14 %

Resolution (Å)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.8-1.831.146820.3791.43499.7
4.88-46.6450.450230.0150.056100

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia23.8.0-g3d57088-dials-3.8data scaling
PDB_EXTRACT3.27data extraction
xia23.8.0-g3d57088-dials-3.8data reduction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 5OPG and PDB ID 5UR8

5opg

5ur8


Resolution: 1.8→46.62 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 4846 5.09 %
Rwork0.1895 --
obs0.1911 95137 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 42 761 6421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086018
X-RAY DIFFRACTIONf_angle_d0.9988238
X-RAY DIFFRACTIONf_dihedral_angle_d6.413863
X-RAY DIFFRACTIONf_chiral_restr0.064953
X-RAY DIFFRACTIONf_plane_restr0.0081057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31761380.29612989X-RAY DIFFRACTION100
1.82-1.840.29371710.28122979X-RAY DIFFRACTION100
1.84-1.860.29911360.26972964X-RAY DIFFRACTION100
1.86-1.890.27651470.25773022X-RAY DIFFRACTION100
1.89-1.910.27061620.25532980X-RAY DIFFRACTION100
1.91-1.940.2481650.25562996X-RAY DIFFRACTION100
1.94-1.970.30461600.25422978X-RAY DIFFRACTION100
1.97-20.29481510.24672987X-RAY DIFFRACTION100
2-2.030.25871470.22732989X-RAY DIFFRACTION100
2.03-2.060.24851700.22082990X-RAY DIFFRACTION100
2.06-2.10.26131750.21882958X-RAY DIFFRACTION100
2.1-2.130.23911550.20793007X-RAY DIFFRACTION100
2.13-2.180.24361610.20252990X-RAY DIFFRACTION100
2.18-2.220.2891610.21373013X-RAY DIFFRACTION100
2.22-2.270.25161740.20682967X-RAY DIFFRACTION100
2.27-2.320.25591870.20332982X-RAY DIFFRACTION100
2.32-2.380.27181950.21142981X-RAY DIFFRACTION100
2.38-2.440.24041440.20553000X-RAY DIFFRACTION100
2.44-2.510.21611640.19883012X-RAY DIFFRACTION100
2.51-2.60.25181370.20183025X-RAY DIFFRACTION100
2.6-2.690.23821330.20243034X-RAY DIFFRACTION100
2.69-2.80.24431590.19123014X-RAY DIFFRACTION100
2.8-2.920.23641460.19343042X-RAY DIFFRACTION100
2.92-3.080.23661910.19022992X-RAY DIFFRACTION100
3.08-3.270.20971760.1833000X-RAY DIFFRACTION100
3.27-3.520.21071730.1733040X-RAY DIFFRACTION100
3.52-3.880.21161330.17083088X-RAY DIFFRACTION100
3.88-4.440.16941680.1423049X-RAY DIFFRACTION100
4.44-5.590.15531730.14753091X-RAY DIFFRACTION100
5.59-46.620.20021940.18583132X-RAY DIFFRACTION98
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)
12.22860.22010.01651.07510.51233.4606-0.02790.5653-0.0827-0.19320.10450.120.121-0.4798-0.06880.253-0.0824-0.04550.54010.08650.247570.08841.005-6.941
21.30530.24940.83350.53130.33981.0728-0.0178-0.12430.09070.0587-0.02570.0186-0.0207-0.11290.04760.17620.010.05380.1570.01950.188684.98852.67543.95
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A22 - 128
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A130 - 220
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A230 - 241
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A243 - 303
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:128 OR RESID 130:220 OR RESID 230:241 OR RESID 243:303 OR RESID 305:344 ) )A305 - 344
6X-RAY DIFFRACTION2( CHAIN B AND RESID 2:2 )B2

+
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