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- PDB-9avf: CCHFV GP38-GnH-DS heterodimer -

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Basic information

Entry
Database: PDB / ID: 9avf
TitleCCHFV GP38-GnH-DS heterodimer
Components
  • GP38
  • Glycoprotein N
KeywordsVIRAL PROTEIN / Crimean-Congo Hemorrhagic Fever Virus / CCHFV / GP38 / Gn / glycoprotein / GP38-Gn / ancestral heterodimer / GPC / fusion loops / accompanying protein
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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcFadden, E. / Ramamohan, A.R. / McLellan, J.S.
Funding support United States, 3items
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
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Cell / Year: 2025
Title: Engineering and structures of Crimean-Congo hemorrhagic fever virus glycoprotein complexes.
Authors: Elizabeth McFadden / Stephanie R Monticelli / Albert Wang / Ajit R Ramamohan / Thomas G Batchelor / Ana I Kuehne / Russell R Bakken / Alexandra L Tse / Kartik Chandran / Andrew S Herbert / Jason S McLellan /
Abstract: Crimean-Congo hemorrhagic fever virus (CCHFV) is a tickborne virus that can cause severe disease in humans with case fatality rates of 10%-40%. Although structures of CCHFV glycoproteins GP38 and Gc ...Crimean-Congo hemorrhagic fever virus (CCHFV) is a tickborne virus that can cause severe disease in humans with case fatality rates of 10%-40%. Although structures of CCHFV glycoproteins GP38 and Gc have provided insights into viral entry and defined epitopes of neutralizing and protective antibodies, the structure of glycoprotein Gn and its interactions with GP38 and Gc have remained elusive. Here, we use structure-guided protein engineering to produce a stabilized GP38-Gn-Gc heterotrimeric glycoprotein complex (GP38-Gn-Gc). A cryo-electron microscopy (cryo-EM) structure of this complex provides the molecular basis for GP38's association on the viral surface, reveals the structure of Gn, and demonstrates that GP38-Gn restrains the Gc fusion loops in the prefusion conformation, facilitated by an N-linked glycan attached to Gn. Immunization with GP38-Gn-Gc conferred 40% protection against lethal IbAr10200 challenge in mice. These data define the architecture of a GP38-Gn-Gc protomer and provide a template for structure-guided vaccine antigen development.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP38
B: Glycoprotein N
C: GP38
D: Glycoprotein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,88711
Polymers73,3384
Non-polymers1,5487
Water1,892105
1
A: GP38
B: Glycoprotein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5546
Polymers36,6692
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint4 kcal/mol
Surface area16510 Å2
MethodPISA
2
C: GP38
D: Glycoprotein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3335
Polymers36,6692
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint1 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.809, 87.010, 128.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein GP38


Mass: 30143.688 Da / Num. of mol.: 2 / Mutation: Q496C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q8JSZ3
#2: Protein Glycoprotein N / Gn / 37 kDa protein / Glycoprotein G2


Mass: 6525.347 Da / Num. of mol.: 2 / Mutation: V562C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q8JSZ3
#3: 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.: 6
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
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% (v/v) TacsimateTM pH 8.0, 20% (v/v) PEG 3,350 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→51.75 Å / Num. obs: 25418 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 51.34 Å2 / CC1/2: 0.992 / Rsym value: 0.107 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2446 / CC1/2: 0.546 / Rsym value: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→51.75 Å / SU ML: 0.3027 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 1274 5.02 %
Rwork0.1965 24126 -
obs0.1987 25400 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 98 105 4690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414660
X-RAY DIFFRACTIONf_angle_d0.83636273
X-RAY DIFFRACTIONf_chiral_restr0.0549738
X-RAY DIFFRACTIONf_plane_restr0.0065780
X-RAY DIFFRACTIONf_dihedral_angle_d15.51971708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.3871120.3232598X-RAY DIFFRACTION97.66
2.6-2.720.34111430.26252655X-RAY DIFFRACTION99.5
2.72-2.860.311260.24162646X-RAY DIFFRACTION100
2.86-3.040.29631420.24682665X-RAY DIFFRACTION100
3.04-3.280.25931470.23262652X-RAY DIFFRACTION100
3.28-3.610.24261590.19332669X-RAY DIFFRACTION100
3.61-4.130.251370.1762692X-RAY DIFFRACTION100
4.13-5.20.18141530.14712709X-RAY DIFFRACTION99.93
5.2-51.750.20431550.1882840X-RAY DIFFRACTION99.3
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)
15.21283334832-0.6675185703620.6009428317225.41729168375-0.8963742828935.75663070722-0.146354543502-0.0261209177869-0.231978163615-0.1159672083950.164774123061-0.8645193785810.1981770761110.751138961411-0.005893477141840.2513284857020.0434865770345-0.005859735944380.45277397169-0.1010837139310.42355991486225.45919369054.0780004995314.0133085944
28.538522389121.621469221630.367688615272.223903703360.9136799886981.44441255892-0.131097672587-1.21396789473-0.2496982090750.5745853567650.0148012023183-0.732649923890.2023902847370.532981279530.1027416056320.4693258387540.0600147062636-0.07627512888740.707956693697-0.02564141741780.45926395217525.90870194756.4208704739726.462987765
33.66972192382-1.678619225880.7351791650355.33826466613-0.1949252941662.627261003530.00166068658623-0.0287349951559-0.1954092935430.0349858187722-0.04939953787590.640482133964-0.0102985217772-0.1125557679270.04956546958890.256347579194-0.01112390904910.01430931176260.349638740984-0.03147635096740.29207349964-2.645395597211.651431351821.1020629965
46.967367193561.230720329371.999004244478.90796178035.307460890347.839474090360.0634431488249-0.20099822444-0.6735497183940.924893858698-0.1160894491281.310879888161.34328389673-0.4014238395870.2133292517340.571369548561-0.04706777516380.09385207178660.5279519238370.07325683023370.631831675736-9.53539146808-1.9987873236829.2226532777
53.62115360244-2.27500975311-3.178191579843.09714187146-0.5033268552326.570711859180.417776432306-1.73900977105-1.415946046852.76615054129-0.127344540685-0.174210689141.29851516713-0.93955702585-0.1918667552072.30961815566-0.589657650583-0.2433443108251.653788313960.008030043792541.4718237615-10.2316507933-5.3079446556537.1985900289
65.720323437812.53686341984.444097782969.132056417726.984130048417.944968089970.763183233074-0.881579206739-0.604693774011.32673316845-0.7513959757650.7050945028861.05817730887-0.984345481941-0.06570733935350.585870290916-0.1023094675890.006954884884790.5207316078230.1127194954970.469435770429-0.4419207682015.2395799859736.4960598051
73.29810850211-1.6057483412-0.4308170066666.501215775341.088848106866.549096769430.2179043243120.2223039743550.442617050801-0.209173349584-0.1253066322470.332599883072-0.343623114528-0.554362607988-0.09973697424240.287932677181-0.03391891661780.08434116962030.4231567056970.04707058658770.39908437485615.43737590788.36527242688-7.64636463882
85.565976686980.3632996944990.0001707056180965.779243502481.353720542995.04851603401-0.01201932310750.2762810802870.0110391854106-0.474075626424-0.1040511783490.2331999750040.293500779977-0.3255163508650.1073380740460.357183324341-0.07054681484950.05722726396350.4130232624240.01080522849650.21811778916120.6980854192-3.51489476426-13.794527044
98.218307252450.2884345620640.6256453235043.72239756912-3.8229431925.98199388079-0.3240129087950.666244051968-1.519182807720.3792618590990.0602658681215-0.2375937243651.79847678517-0.2173690089720.3658650802961.438202146370.168378214780.02524979799860.547013915542-0.04805243123810.67848694846333.6621884094-27.1005025494-6.06488013277
107.245510000011.882918432262.244299674238.816834567214.25636046095.19329495420.1713496670780.72577403338-0.1621476056450.118322001290.116529800602-0.9762421987660.09163487203780.782706911795-0.2244310839360.6960394098830.070567855973-0.01147546379080.4735099437360.0644933596710.35934841257437.2746185055-14.5044810057-11.5836351083
113.31389622171-0.133030988001-0.7587032600276.242304834280.6369836833353.765894962290.04427735689820.0202982656298-0.3037353649570.852792488332-0.0120524421556-0.3290908071111.285497561020.311337283784-0.05807545922980.8647124755070.0516551971845-0.01786851722330.452033392456-0.0245898983220.28213735038830.398417895-16.0316052028-7.41243735961
122.726685500581.84646250759-2.491449789745.60985165416-5.64249297245.86989647299-0.4914635607220.760675942736-0.0443703145962-1.33343718848-0.586653692684-0.7755709839141.06860294220.01880687046430.6384195366191.56136656657-0.9573600867930.5007843601820.3345617882040.07859087168080.75839840532822.5235430261-25.5182840488-18.9474389063
132.28034206153-0.399403343309-1.842259516689.2846914746-1.787279685782.06287777613-0.0478822368070.178105269538-0.85891247365-1.38776730172-0.3820279509291.24452141.38690507795-0.8387436532690.3060685996971.28578233418-0.409756610610.1412822288780.992984278671-0.2054230850410.78026975575216.3393963984-26.3919389866-16.8789571199
143.82830281539-1.0068969858-2.35192992190.3233078367031.050043970934.3732258992-0.270143813923-0.09476856875180.321864587881.865920072110.219950331629-0.170076535722-0.2272823082650.1366506617980.03196356019670.903321792824-0.02535687564130.05166568673630.567184848574-0.02133738806050.48139560675529.872173438-3.36508172127-26.9256314401
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 252 through 308 )AA252 - 3081 - 57
22chain 'A' and (resid 309 through 364 )AA309 - 36458 - 102
33chain 'A' and (resid 365 through 514 )AA365 - 514103 - 252
44chain 'B' and (resid 552 through 563 )BE552 - 5631 - 12
55chain 'B' and (resid 564 through 568 )BE564 - 56813 - 17
66chain 'B' and (resid 569 through 584 )BE569 - 58418 - 33
77chain 'C' and (resid 253 through 346 )CG253 - 3461 - 76
88chain 'C' and (resid 347 through 381 )CG347 - 38177 - 111
99chain 'C' and (resid 382 through 402 )CG382 - 402112 - 132
1010chain 'C' and (resid 403 through 431 )CG403 - 431133 - 161
1111chain 'C' and (resid 432 through 509 )CG432 - 509162 - 239
1212chain 'D' and (resid 550 through 556 )DJ550 - 5561 - 7
1313chain 'D' and (resid 557 through 576 )DJ557 - 5768 - 27
1414chain 'D' and (resid 577 through 590 )DJ577 - 59028 - 41

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