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- PDB-6vkf: CCHFV GP38 (IbAr10200) -

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Basic information

Entry
Database: PDB / ID: 6vkf
TitleCCHFV GP38 (IbAr10200)
ComponentsGP38
KeywordsVIRAL PROTEIN / secretory / viral / glycoprotein
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / virion component => GO:0044423 / host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 ...virus-mediated perturbation of host defense response => GO:0019049 / virion component => GO:0044423 / host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Nairovirus M polyprotein-like / Nairovirus GP38 / : ...: / : / : / : / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Nairovirus M polyprotein-like / Nairovirus GP38 / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Glycoprotein G2 / Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever orthonairovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.524 Å
AuthorsMishra, A.K. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Virol. / Year: 2020
Title: Structure and Characterization of Crimean-Congo Hemorrhagic Fever Virus GP38.
Authors: Mishra, A.K. / Moyer, C.L. / Abelson, D.M. / Deer, D.J. / El Omari, K. / Duman, R. / Lobel, L. / Lutwama, J.J. / Dye, J.M. / Wagner, A. / Chandran, K. / Cross, R.W. / Geisbert, T.W. / ...Authors: Mishra, A.K. / Moyer, C.L. / Abelson, D.M. / Deer, D.J. / El Omari, K. / Duman, R. / Lobel, L. / Lutwama, J.J. / Dye, J.M. / Wagner, A. / Chandran, K. / Cross, R.W. / Geisbert, T.W. / Zeitlin, L. / Bornholdt, Z.A. / McLellan, J.S.
History
DepositionJan 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP38
B: GP38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9786
Polymers60,4842
Non-polymers1,4944
Water18010
1
A: GP38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0913
Polymers30,2421
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GP38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8873
Polymers30,2421
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.350, 97.870, 66.010
Angle α, β, γ (deg.)90.000, 103.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GP38


Mass: 30241.828 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: A0A1V0G0G3, UniProt: Q8JSZ3*PLUS
#2: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate pH 5.5, PEG 400, PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.979
SYNCHROTRONDiamond I2322.7551
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 9, 2018
DECTRIS PILATUS 12M2PIXELFeb 6, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
22.75511
Reflection

Entry-ID: 6VKF

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Diffraction-IDNet I/σ(I)
2.52-51.48125110973.20.998112.6
2.79-64.853830295.4150.999212
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
2.52-2.632.528680.8151
2.79-2.941.525840.7332

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
PHASERphasing
SHELXDphasing
PHENIXmodel building
BUCCANEERmodel building
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.524→51.481 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.1
RfactorNum. reflection% reflection
Rfree0.2558 1206 4.81 %
Rwork0.2227 --
obs0.2243 25070 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.44 Å2 / Biso mean: 92.734 Å2 / Biso min: 47.5 Å2
Refinement stepCycle: final / Resolution: 2.524→51.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 98 10 3901
Biso mean--136.23 68.43 -
Num. residues----472
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.524-2.62510.36821380.3177265998
2.6251-2.74460.3421350.2903265797
2.7446-2.88920.31531240.2823257295
2.8892-3.07020.3181990.3065269297
3.0702-3.30730.32041240.2654271198
3.3073-3.640.29371380.2447258295
3.64-4.16650.25461510.2231268298
4.1665-5.24850.20561510.1757261296
5.2485-51.4810.23091460.2001269797
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)
13.1597-0.2198-0.52887.2648-0.07225.05110.10550.2947-0.0988-0.38680.1102-0.7760.0450.52640.11030.855-0.06140.2190.5732-0.09680.547843.357771.8414-16.3584
22.52970.7028-0.88475.3554-3.17564.0857-0.0887-0.0603-0.20510.45290.27180.18140.07060.03760.0751.03420.10040.22850.4726-0.01230.676634.095452.0180.798
34.63250.26750.41633.9433-0.76085.3042-0.0382-0.0549-0.4146-0.4777-0.1437-0.48430.23480.47930.26180.97010.07160.31670.53470.05950.616141.599629.128510.5992
47.6831-0.4648-3.71310.99960.81251.9819-0.2836-1.2075-0.6016-0.6524-0.1942-1.8680.03651.29230.72771.08730.0880.42771.15940.24991.474659.687929.879112.7523
52.8407-0.8056-0.05723.75740.50473.70260.0097-0.72590.08810.85540.0171-0.77340.25161.30630.39071.3346-0.01180.0911.09420.03251.035247.707334.732730.4243
63.2173-2.0588-2.60755.02742.70634.10460.18790.0991.6625-0.07350.0905-2.4136-0.621.7279-0.20351.9233-0.3425-0.12731.5339-0.00991.468347.067347.424341.6438
75.0235-0.9209-2.45344.41130.88915.9525-0.2578-0.7366-0.11941.19250.0114-0.4949-0.63020.43210.14581.37050.00260.03541.130.01250.668740.823337.268534.1161
83.0851-2.5143-0.08223.6338-1.46531.0548-0.0714-0.7639-0.53870.76320.35120.82980.76950.2665-0.02862.83990.22410.64921.2618-0.46150.633834.404739.176847.4941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 134 )A5 - 134
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 262 )A135 - 262
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 61 )B3 - 61
4X-RAY DIFFRACTION4chain 'B' and (resid 62 through 95 )B62 - 95
5X-RAY DIFFRACTION5chain 'B' and (resid 96 through 155 )B96 - 155
6X-RAY DIFFRACTION6chain 'B' and (resid 156 through 171 )B156 - 171
7X-RAY DIFFRACTION7chain 'B' and (resid 172 through 238 )B172 - 238
8X-RAY DIFFRACTION8chain 'B' and (resid 239 through 267 )B239 - 267

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