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- PDB-8ddk: CCHFV GP38 Hoti/Kosovo bound with CC5_17 -

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Basic information

Entry
Database: PDB / ID: 8ddk
TitleCCHFV GP38 Hoti/Kosovo bound with CC5_17
Components
  • Envelopment polyprotein
  • Heavy Chain CC5-17
  • Light Chain CC5_17
KeywordsVIRAL PROTEIN / Crimean-Congo Hemorrhagic Fever / CCHFV / Glycoprotein / GP38 / Hoti / Kosovo / 13G8 / Fab / CC5-17 / mAb
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / virus-mediated perturbation of host defense response / 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 speciesHomo sapiens (human)
Crimean-Congo hemorrhagic fever orthonairovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.86 Å
AuthorsDurie, I.A. / Bergeron, E. / Pegan, S.D. / McGuire, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109008 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151006 United States
Defense Threat Reduction Agency (DTRA)HDTRA12110005 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural characterization of protective non-neutralizing antibodies targeting Crimean-Congo hemorrhagic fever virus.
Authors: Durie, I.A. / Tehrani, Z.R. / Karaaslan, E. / Sorvillo, T.E. / McGuire, J. / Golden, J.W. / Welch, S.R. / Kainulainen, M.H. / Harmon, J.R. / Mousa, J.J. / Gonzalez, D. / Enos, S. / Koksal, I. ...Authors: Durie, I.A. / Tehrani, Z.R. / Karaaslan, E. / Sorvillo, T.E. / McGuire, J. / Golden, J.W. / Welch, S.R. / Kainulainen, M.H. / Harmon, J.R. / Mousa, J.J. / Gonzalez, D. / Enos, S. / Koksal, I. / Yilmaz, G. / Karakoc, H.N. / Hamidi, S. / Albay, C. / Spengler, J.R. / Spiropoulou, C.F. / Garrison, A.R. / Sajadi, M.M. / Bergeron, E. / Pegan, S.D.
History
DepositionJun 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy Chain CC5-17
B: Light Chain CC5_17
C: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1815
Polymers80,3593
Non-polymers1,8222
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.676, 175.676, 92.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Heavy Chain CC5-17


Mass: 26087.045 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: Protein Envelopment polyprotein / M polyprotein


Mass: 31068.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever orthonairovirus
Production host: Homo sapiens (human) / References: UniProt: A0A7T6Y557

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Antibody / Non-polymers , 2 types, 2 molecules B

#2: Antibody Light Chain CC5_17


Mass: 23203.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4[DManpa1-3]DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3-2-2/a4-b1_b3-c1_b4-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Details

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: 4.45 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG1000, and 0.1M HEPES pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 13942 / % possible obs: 98.59 % / Redundancy: 7.8 % / CC1/2: 0.881 / Rpim(I) all: 0.1 / Net I/σ(I): 21.8
Reflection shellResolution: 3.85→3.92 Å / Num. unique obs: 1363 / CC1/2: 0.763 / CC star: 0.93 / Rpim(I) all: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DC5

8dc5


Resolution: 3.86→43.07 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 42.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3347 644 4.7 %
Rwork0.3037 13055 -
obs0.3052 13699 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 496.77 Å2 / Biso mean: 247.1599 Å2 / Biso min: 92.86 Å2
Refinement stepCycle: final / Resolution: 3.86→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 122 1 4668
Biso mean--287.49 232.59 -
Num. residues----578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.86-4.160.36451020.32882486258895
4.16-4.570.33381260.30852576270298
4.57-5.240.33961360.29042600273698
5.24-6.590.39891330.34232662279599
6.59-43.070.30951470.28982731287897
Refinement TLS params.Method: refined / Origin x: 20.1997 Å / Origin y: -55.4393 Å / Origin z: 0.1314 Å
111213212223313233
T1.9444 Å2-0.2127 Å2-0.2901 Å2-1.6519 Å20.0634 Å2--1.1331 Å2
L2.3462 °23.5355 °20.1527 °2-8.8704 °21.8277 °2--1.4449 °2
S-0.259 Å °-0.0454 Å °0.4813 Å °-1.093 Å °0.113 Å °-0.3725 Å °-1.01 Å °0.4476 Å °0.1338 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 226
2X-RAY DIFFRACTION1allB2 - 201
3X-RAY DIFFRACTION1allC255 - 517
4X-RAY DIFFRACTION1allC518 - 523
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allF1

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