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- PDB-8dcy: CCHFV GP38 Hoti/Kosovo bound with 13G8 Fab -

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Basic information

Entry
Database: PDB / ID: 8dcy
TitleCCHFV GP38 Hoti/Kosovo bound with 13G8 Fab
Components
  • 13G8 Heavy Chain
  • 13G8 Light Chain
  • Envelopment polyprotein
KeywordsVIRAL PROTEIN / Crimean-Congo Hemorrhagic Fever / CCHFV / Glycoprotein / GP38 / Hoti / Kosovo / 13G8 / Fab
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Crimean-Congo hemorrhagic fever orthonairovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 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 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 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: 13G8 Heavy Chain
B: 13G8 Light Chain
C: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2635
Polymers79,4153
Non-polymers8492
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.919, 175.919, 93.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody 13G8 Heavy Chain


Mass: 25154.201 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)
#2: Antibody 13G8 Light Chain


Mass: 23191.758 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: 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
#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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.56 Å3/Da / Density % sol: 73.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 1.1M sodium malonate, 0.1M HEPES pH 7.0, and 0.5% Jeffamine ED-2001

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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: 3.6→50 Å / Num. obs: 17277 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 184 Å2 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.052 / Rrim(I) all: 0.172 / Χ2: 1.499 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.6610.21.7418290.780.5541.8281.395100
3.66-3.73112.0978670.7720.6522.1981.171100
3.73-3.811.21.6388260.810.5041.7151.055100
3.8-3.8810.91.718540.8330.5371.7941.288100
3.88-3.9610.91.3718380.8550.431.4381.558100
3.96-4.0511.10.9518500.8610.2960.9971.202100
4.05-4.1611.10.6948360.9550.2160.7271.277100
4.16-4.27110.5588590.9540.1740.5851.332100
4.27-4.39110.3858450.9790.120.4041.535100
4.39-4.54110.3898530.9680.1210.4081.663100
4.54-4.710.90.2978580.9920.0940.3111.78100
4.7-4.8910.90.2538570.9920.080.2661.801100
4.89-5.11110.2698620.9850.0840.2821.886100
5.11-5.3810.90.2338540.9850.0740.2451.797100
5.38-5.7110.80.2078620.9950.0660.2181.64399.9
5.71-6.1510.80.1838770.9920.0580.1921.73199.9
6.15-6.7710.80.1598790.9930.050.1671.68699.9
6.77-7.7510.80.1138970.9960.0350.1181.649100
7.75-9.7510.50.0648940.9980.020.0671.414100
9.75-509.80.0559800.9990.0180.0581.09999.9

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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: 3.62→45.06 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2993 801 4.72 %
Rwork0.2807 16165 -
obs0.2816 16966 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 374.87 Å2 / Biso mean: 184.0648 Å2 / Biso min: 74.79 Å2
Refinement stepCycle: final / Resolution: 3.62→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 56 3 5109
Biso mean--173.67 143.21 -
Num. residues----651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.62-3.840.42571330.42012487262093
3.84-4.140.44641320.39142642277499
4.14-4.550.31721350.29062680281599
4.55-5.210.271270.26822722284999
5.21-6.560.31821430.300527282871100
6.56-45.060.2511310.238129063037100
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)
13.52592.2783-2.3136.8009-0.36662.3714-0.58840.09562.2005-0.94721.20390.1818-1.58431.4096-0.56843.31041.5080.09142.4707-1.26951.5649-29.0939-34.566435.2524
23.9478-2.26892.50433.118-0.92794.2065-1.2237-1.00491.13991.42820.5325-0.5296-0.2493-0.37040.57722.83440.6497-0.3561.5672-0.17231.3409-20.4031-41.578731.0759
35.4209-3.65141.98812.72660.0323.1205-1.299-0.97790.3014-0.04280.58621.0473-1.0693-0.29860.28582.37190.60390.24732.5687-0.17841.5959-36.0054-27.609628.5687
47.5315-3.178-0.97179.4865-5.87454.9564-0.47440.2986-3.32270.62723.19523.07720.2901-4.1352-1.97652.68780.2708-0.60473.1901-0.38583.1727-65.559-29.109115.7592
50.981-0.60510.46190.960.34680.8554-1.2898-1.49631.51810.8491.1806-0.8039-1.18150.2965-1.2543.70123.08890.5813.8092-0.54781.3314-44.7792-24.055226.1664
63.0205-2.24953.53895.4718-2.05388.7764-0.3287-3.2317-0.42460.47161.24410.7383-1.2603-3.336-0.79173.51212.02960.11013.66290.10251.5411-50.4571-26.354826.9231
77.3254-1.62731.61986.7057-1.80034.4291-0.42720.0160.13610.77540.46220.2456-0.66460.0239-0.00591.56160.46190.04261.28220.12171.1355-29.7725-52.104114.1464
87.9926-3.36323.14683.9465-2.49294.1760.0253-0.8455-1.51120.80961.06970.43010.7203-0.8241-1.19982.34650.5142-0.09072.25630.13011.2194-28.6511-48.838616.5943
93.8002-1.6890.56591.2546-0.69610.5324-0.8535-0.70131.40990.48220.9213-0.1517-2.443-1.75230.38722.68531.0133-0.042.25720.19741.5076-51.549-28.70613.4829
108.07090.13310.6422.4998-1.8163.9789-1.1829-1.68660.97251.22051.25571.9714-1.5255-0.6694-0.17212.34340.9908-0.00262.01950.13011.5766-49.4511-22.069410.5648
117.1793-3.2137-1.61778.73331.72764.436-0.84770.04680.9591-0.26751.2727-0.2216-1.2096-1.85990.53572.70830.8021-0.06272.16810.17481.6812-57.8937-21.95584.5458
126.8185-6.64544.74887.3066-3.84267.1609-0.9822-1.3180.73451.58450.6369-0.2998-1.5637-0.26840.36611.55660.1966-0.05581.0957-0.04411.0094-6.4946-64.290336.7404
139.2824-0.9960.44267.05541.05146.13070.0155-0.3441-0.1344-0.311-0.0828-0.32340.22070.62030.0920.96260.01140.14220.88190.10630.68649.7855-86.314635.3751
143.8773-5.53333.36628.5405-5.76474.14341.00222.4213-0.8818-3.56050.2715-0.93551.53760.2327-0.57960.9669-0.08830.34692.0152-0.0360.953717.8341-93.270528.1006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 23 )A2 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 107 )A24 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 131 )A108 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 143 )A132 - 143
5X-RAY DIFFRACTION5chain 'A' and (resid 144 through 161 )A144 - 161
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 219 )A162 - 219
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 74 )B1 - 74
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 100 )B75 - 100
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 125 )B101 - 125
10X-RAY DIFFRACTION10chain 'B' and (resid 126 through 189 )B126 - 189
11X-RAY DIFFRACTION11chain 'B' and (resid 190 through 210 )B190 - 210
12X-RAY DIFFRACTION12chain 'C' and (resid 255 through 363 )C255 - 363
13X-RAY DIFFRACTION13chain 'C' and (resid 364 through 502 )C364 - 502
14X-RAY DIFFRACTION14chain 'C' and (resid 503 through 516 )C503 - 516

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