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- PDB-8dc5: CCHFV GP38 Hoti/Kosovo -

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Basic information

Entry
Database: PDB / ID: 8dc5
TitleCCHFV GP38 Hoti/Kosovo
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Crimean-Congo Hemorrhagic Fever / CCHFV / Glycoprotein / GP38 / Hoti / Kosovo
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
IODIDE ION / Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever orthonairovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 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 15, 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 1.2Nov 6, 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: Envelopment polyprotein
B: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,53010
Polymers62,1372
Non-polymers1,3928
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.633, 75.322, 62.218
Angle α, β, γ (deg.)90.000, 110.410, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21B-715-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 258 through 326 or resid 345...
21(chain B and (resid 258 through 326 or resid 345...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 258 through 326 or resid 345...A258 - 326
121(chain A and (resid 258 through 326 or resid 345...A345 - 371
131(chain A and (resid 258 through 326 or resid 345...A378 - 381
141(chain A and (resid 258 through 326 or resid 345...A386 - 407
151(chain A and (resid 258 through 326 or resid 345...A436 - 512
161(chain A and (resid 258 through 326 or resid 345...A514 - 515
211(chain B and (resid 258 through 326 or resid 345...B258 - 326
221(chain B and (resid 258 through 326 or resid 345...B345 - 396
231(chain B and (resid 258 through 326 or resid 345...B401 - 407
241(chain B and (resid 258 through 326 or resid 345...B409 - 414
251(chain B and (resid 258 through 326 or resid 345...B436 - 492
261(chain B and (resid 258 through 326 or resid 345...B501 - 512
271(chain B and (resid 258 through 326 or resid 345...B513 - 514

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 31068.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever orthonairovirus
Production host: Homo sapiens (human) / References: UniProt: A0A7T6Y557
#2: 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.: 4 / 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
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.4M NH4I

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11973 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 108.8 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.072 / Rrim(I) all: 0.134 / Χ2: 2.759 / Net I/σ(I): 17 / Num. measured all: 42451
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.263.80.686120.7570.4080.7941.176100
3.26-3.313.70.5735940.8770.3430.6691.349100
3.31-3.383.80.4076060.9410.2440.4751.366100
3.38-3.453.70.3816290.9290.2340.4491.90599.7
3.45-3.523.70.4025740.9340.2460.4722.14399.5
3.52-3.63.70.5646340.9240.3410.662.631100
3.6-3.693.10.2465780.9310.1670.2984.29698.6
3.69-3.793.50.4075950.9310.2530.483.79499.3
3.79-3.913.60.1646290.9710.1020.1932.53299.8
3.91-4.033.60.1555900.9830.0980.1843.41499.3
4.03-4.183.70.1176040.9830.0710.1372.47599.5
4.18-4.343.60.095940.9880.0550.1062.75899.5
4.34-4.543.60.0896180.9890.0550.1053.193100
4.54-4.783.50.0776130.990.0490.0913.55399.2
4.78-5.083.50.0796060.9870.0490.0943.24699.5
5.08-5.473.50.0816040.9880.0510.0963.38299.7
5.47-6.023.50.096070.9880.0560.1063.4799.5
6.02-6.893.50.0946330.9830.0580.1113.04999.7
6.89-8.673.20.0846140.9840.0560.1013.77599.5
8.67-502.90.0914390.9730.0660.1132.54368.1

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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: 6VKF

6vkf


Resolution: 3.21→29.16 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3032 602 5.07 %
Rwork0.2753 11283 -
obs0.2767 11885 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.49 Å2 / Biso mean: 121.7082 Å2 / Biso min: 58.32 Å2
Refinement stepCycle: final / Resolution: 3.21→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 60 45 3621
Biso mean--153.94 94.76 -
Num. residues----436
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1224X-RAY DIFFRACTION8.768TORSIONAL
12B1224X-RAY DIFFRACTION8.768TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.21-3.320.42111490.3363281197
3.54-4.050.37891490.3467281497
4.05-5.090.26631560.2409289199
5.09-29.160.27571480.2598276793
Refinement TLS params.Method: refined / Origin x: 21.2886 Å / Origin y: -20.2044 Å / Origin z: -8.3918 Å
111213212223313233
T0.6074 Å20.0048 Å2-0.0192 Å2-0.7045 Å2-0.0383 Å2--0.6192 Å2
L1.7434 °2-0.2509 °2-0.4328 °2-1.3425 °20.1507 °2--1.8642 °2
S0.1418 Å °-0.0173 Å °0.0337 Å °-0.0361 Å °-0.1095 Å °0.0122 Å °0.1234 Å °0.2577 Å °-0.0332 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA257 - 513
2X-RAY DIFFRACTION1allA514 - 515
3X-RAY DIFFRACTION1allB258 - 512
4X-RAY DIFFRACTION1allB513 - 514
5X-RAY DIFFRACTION1allF6 - 342
6X-RAY DIFFRACTION1allE1 - 8

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