[English] 日本語
Yorodumi
- PDB-8vvl: CCHFV GP38 bound to c13G8 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vvl
TitleCCHFV GP38 bound to c13G8 Fab
Components
  • GP38
  • c13G8 Fab Heavy Chain
  • c13G8 Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / CCHFV / GP38 / Antibody / Immunology / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc ...Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
: / Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHjorth, C.K. / Mishra, A.K. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152246 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI142777 United States
CitationJournal: Cell Rep / Year: 2024
Title: Crimean-Congo hemorrhagic fever survivors elicit protective non-neutralizing antibodies that target 11 overlapping regions on glycoprotein GP38.
Authors: Olivia S Shin / Stephanie R Monticelli / Christy K Hjorth / Vladlena Hornet / Michael Doyle / Dafna Abelson / Ana I Kuehne / Albert Wang / Russell R Bakken / Akaash K Mishra / Marissa ...Authors: Olivia S Shin / Stephanie R Monticelli / Christy K Hjorth / Vladlena Hornet / Michael Doyle / Dafna Abelson / Ana I Kuehne / Albert Wang / Russell R Bakken / Akaash K Mishra / Marissa Middlecamp / Elizabeth Champney / Lauran Stuart / Daniel P Maurer / Jiannan Li / Jacob Berrigan / Jennifer Barajas / Stephen Balinandi / Julius J Lutwama / Leslie Lobel / Larry Zeitlin / Laura M Walker / John M Dye / Kartik Chandran / Andrew S Herbert / Noel T Pauli / Jason S McLellan /
Abstract: Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, exclusive to Nairoviridae, is a target of ...Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, exclusive to Nairoviridae, is a target of protective antibodies and is a key antigen in preclinical vaccine candidates. Here, we isolate 188 GP38-specific antibodies from human survivors of infection. Competition experiments show that these antibodies bind across 5 distinct antigenic sites, encompassing 11 overlapping regions. Additionally, we show structures of GP38 bound with 9 of these antibodies targeting different antigenic sites. Although these GP38-specific antibodies are non-neutralizing, several display protective efficacy equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and may inform the development of broadly effective CCHFV antibody therapeutics.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GP38
H: c13G8 Fab Heavy Chain
L: c13G8 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,07718
Polymers77,5843
Non-polymers1,49415
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-160 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.429, 67.629, 140.983
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Space group name H-MI121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein GP38


Mass: 30241.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Strain: IbAr10200 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q8JSZ3

-
Antibody , 2 types, 2 molecules HL

#2: Antibody c13G8 Fab Heavy Chain


Mass: 24215.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody c13G8 Fab Light Chain


Mass: 23126.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

-
Non-polymers , 4 types, 636 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 0.01 M Cobalt chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→45.16 Å / Num. obs: 81877 / % possible obs: 94.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.31 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03316 / Rpim(I) all: 0.03316 / Rrim(I) all: 0.0469 / Net I/σ(I): 9.5
Reflection shellResolution: 1.804→1.868 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2688 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8008 / CC1/2: 0.915 / CC star: 0.978 / Rpim(I) all: 0.2688 / Rrim(I) all: 0.3801 / % possible all: 92.89

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.16 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 4111 5.03 %
Rwork0.1996 --
obs0.2004 81791 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5121 0 79 623 5823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045304
X-RAY DIFFRACTIONf_angle_d0.7527199
X-RAY DIFFRACTIONf_dihedral_angle_d6.145730
X-RAY DIFFRACTIONf_chiral_restr0.054818
X-RAY DIFFRACTIONf_plane_restr0.006899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.38191540.32852459X-RAY DIFFRACTION88
1.83-1.850.35091150.29862699X-RAY DIFFRACTION95
1.85-1.870.29281470.27892686X-RAY DIFFRACTION95
1.87-1.90.31311340.26462720X-RAY DIFFRACTION95
1.9-1.920.28481410.26152712X-RAY DIFFRACTION96
1.92-1.950.29181530.24452689X-RAY DIFFRACTION96
1.95-1.980.2561500.25932700X-RAY DIFFRACTION96
1.98-2.010.27561290.24142713X-RAY DIFFRACTION96
2.01-2.040.2491360.23962661X-RAY DIFFRACTION95
2.04-2.080.24941210.22732603X-RAY DIFFRACTION92
2.08-2.110.25391500.22132459X-RAY DIFFRACTION87
2.11-2.160.24181620.21722679X-RAY DIFFRACTION96
2.16-2.20.25861430.20372751X-RAY DIFFRACTION97
2.2-2.250.25981530.21172723X-RAY DIFFRACTION97
2.25-2.30.23421270.2022731X-RAY DIFFRACTION97
2.3-2.360.24391520.20262719X-RAY DIFFRACTION97
2.36-2.420.22891420.21112743X-RAY DIFFRACTION96
2.42-2.490.23571640.22482641X-RAY DIFFRACTION95
2.49-2.570.23841430.22242418X-RAY DIFFRACTION86
2.57-2.660.27661400.21442749X-RAY DIFFRACTION97
2.66-2.770.21811360.2132766X-RAY DIFFRACTION97
2.77-2.90.2431370.20992754X-RAY DIFFRACTION97
2.9-3.050.23171460.19952755X-RAY DIFFRACTION97
3.05-3.240.22791260.19182693X-RAY DIFFRACTION94
3.24-3.490.18391160.17982566X-RAY DIFFRACTION90
3.49-3.840.18451580.17052796X-RAY DIFFRACTION98
3.84-4.40.16871520.15672773X-RAY DIFFRACTION97
4.4-5.540.13471280.16242584X-RAY DIFFRACTION90
5.54-45.160.20851560.21372738X-RAY DIFFRACTION93
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)
13.8553-1.24791.14882.2496-0.07452.24240.12060.6955-0.5191-0.134-0.03760.10930.22020.1852-0.05120.21680.0016-0.00340.473-0.07930.244-41.507715.1813-17.139
25.55460.214-0.64724.40410.28944.32180.09711.21760.7224-0.47820.0362-0.3296-0.63970.6639-0.21930.3432-0.10720.01940.8090.04390.3716-29.295321.9855-17.9644
36.0377-1.54010.18793.0763-1.08333.2360.10340.0641-0.4190.057-0.0578-0.31160.05140.2817-0.05970.1799-0.0319-0.0120.4436-0.08630.4481-14.626310.0158-2.8256
45.0971-0.50.72281.49070.11982.9010.05180.2399-0.2438-0.1761-0.05330.0640.02320.0384-0.01720.20770.0336-0.00320.23-0.02560.1575-67.220224.4468-27.7321
52.33460.74620.78267.34460.27912.90650.06360.19910.08010.05730.12850.22-0.1159-0.0307-0.1660.15120.01840.02710.34050.02560.1572-92.056542.4464-30.4835
61.8937-1.87050.11684.8204-0.16761.4578-0.0453-0.14650.11370.03830.00540.1279-0.2228-0.29810.0160.17290.0084-0.00640.3391-0.02690.1744-69.141631.4108-5.5969
75.2847-4.945-1.15793.99590.43630.4938-0.041-0.28910.20030.21650.0624-0.0968-0.2012-0.1150.00160.22680.0295-0.00110.3628-0.03520.2124-75.095732.9436-8.1039
82.44110.27921.06222.00720.76514.54220.0774-0.3628-0.15920.14010.02470.37710.2979-1.0527-0.06570.31-0.00460.0610.5410.08690.2936-104.056839.2778-19.7812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 251 through 308 )
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 381 )
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 509 )
4X-RAY DIFFRACTION4chain 'H' and (resid 2 through 119 )
5X-RAY DIFFRACTION5chain 'H' and (resid 120 through 214 )
6X-RAY DIFFRACTION6chain 'L' and (resid 2 through 75 )
7X-RAY DIFFRACTION7chain 'L' and (resid 76 through 113 )
8X-RAY DIFFRACTION8chain 'L' and (resid 114 through 213 )

+
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