[English] 日本語
Yorodumi
- PDB-9l2k: The crystal structure of SFTSV Gn and SD22 antibody complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l2k
TitleThe crystal structure of SFTSV Gn and SD22 antibody complex
Components
  • Envelopment polyprotein
  • SD22 heavy chain
  • SD22 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SD22 / SFTSV / Antibody / Gn / Severe fever with thrombocytopenia virus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia syndrome virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsShi, W.F. / Quan, C.S. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325003 China
CitationJournal: To Be Published
Title: Molecular mechanism of potently neutralizing human monoclonal antibodies against severe fever with thrombocytopenia virus infection
Authors: Quan, C.S. / Qi, J.X. / Shi, W.F.
History
DepositionDec 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelopment polyprotein
H: SD22 heavy chain
L: SD22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2425
Polymers85,2313
Non-polymers1,0112
Water00
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)64.471, 70.346, 177.469
Angle α, β, γ (deg.)90.000, 90.177, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 37958.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe fever with thrombocytopenia syndrome virus
Production host: Homo sapiens (human) / References: UniProt: A0A1S6K8S9
#2: Antibody SD22 heavy chain


Mass: 23785.525 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: Antibody SD22 light chain


Mass: 23487.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 4 %v/v(+/-)-2-Methy1-2,4-pentanediol, 0.1 M Citric acid pH 3.5, 20 % w/v Polyethylene glycol 1,500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 19950 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.186 / Net I/σ(I): 12.322
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.299 / Num. unique obs: 16920 / CC1/2: 0.749

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→41.94 Å / Cross valid method: FREE R-VALUE / σ(F): 40.12 / Phase error: 33.1553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3122 892 5.27 %
Rwork0.304 16028 -
obs0.3059 16920 84.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 2.78→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 67 0 4262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324370
X-RAY DIFFRACTIONf_angle_d0.715914
X-RAY DIFFRACTIONf_chiral_restr0.0448634
X-RAY DIFFRACTIONf_plane_restr0.0066764
X-RAY DIFFRACTIONf_dihedral_angle_d14.74961573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.960.3174560.3451353X-RAY DIFFRACTION40.8
2.96-3.190.3341110.32052304X-RAY DIFFRACTION69.19
3.19-3.510.28971450.30462886X-RAY DIFFRACTION87.77
3.51-4.020.33091430.29323200X-RAY DIFFRACTION95.1
4.02-5.060.26561700.28153138X-RAY DIFFRACTION94.04
5.06-41.940.33031880.3293226X-RAY DIFFRACTION93.83
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)
10.0117503286181-0.0210879149373-0.005761565820550.03290995905170.0101787965620.008222881451040.04500509894110.02740851329970.00301612785406-0.0398104444105-0.0156705789118-0.028002988780.0268842259570.02804637930010.1048644656880.08270116573830.102216242146-0.02187234401170.0875507977353-0.01341934596270.10509739699939.350.02268.706
20.00512793264634-0.002856524670860.001154103668910.0020338941853-0.002574830109310.006093965208060.0002139755904140.00185385179507-0.00039097113-0.0414940716158-0.002518036232060.0146303771220.00462555363060.007214465514680.005698129597630.3054814370080.131913436669-0.09989682978250.172425561004-0.05027544619780.1324636294522.011-4.68431.901
30.00684507438546-0.00231494158934-0.001248697289040.001967602189930.002977702690880.004876045480890.000405020898321-0.000625069799066-0.005133047-0.00347484287551-0.006795283034060.00849986645-0.0161552635916-0.0322852869815-0.0087479482250.2100205958930.151561085511-0.07474260385170.221777321074-0.05268282333860.1231824949074.971.72845.123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 21:341 )A21 - 341
2X-RAY DIFFRACTION2( CHAIN H AND RESID 1:121 )H1 - 121
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:108 )L1 - 108

+
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