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- PDB-5xeb: Structure of the envelope glycoprotein of Dhori virus -

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Basic information

Entry
Database: PDB / ID: 5xeb
TitleStructure of the envelope glycoprotein of Dhori virus
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / Dhori virus / glycoprotein / fuion machine
Function / homologyBaculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein / symbiont-mediated perturbation of host process / viral envelope / virion membrane / membrane / Envelope glycoprotein
Function and homology information
Biological speciesDhori virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsPeng, R. / Shi, Y. / Qi, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China81641001 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of human-infectingThogotovirusfusogens support a common ancestor with insect baculovirus
Authors: Peng, R. / Zhang, S. / Cui, Y. / Shi, Y. / Gao, G.F. / Qi, J.
History
DepositionApr 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct_keywords
Item: _citation.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
C: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6837
Polymers160,7983
Non-polymers8854
Water3,621201
1
A: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,1259
Polymers160,7983
Non-polymers1,3276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30210 Å2
ΔGint-208 kcal/mol
Surface area51670 Å2
MethodPISA
2
B: Envelope glycoprotein
hetero molecules

B: Envelope glycoprotein
hetero molecules

B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4626
Polymers160,7983
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area29470 Å2
ΔGint-216 kcal/mol
Surface area51130 Å2
MethodPISA
3
C: Envelope glycoprotein
hetero molecules

C: Envelope glycoprotein
hetero molecules

C: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4626
Polymers160,7983
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area29030 Å2
ΔGint-204 kcal/mol
Surface area52270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.729, 106.729, 134.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-800-

HOH

21B-753-

HOH

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Components

#1: Protein Envelope glycoprotein


Mass: 53599.336 Da / Num. of mol.: 3 / Fragment: UNP residues 21-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dhori virus (strain Indian/1313/61) / Strain: Indian/1313/61 / Gene: P4 / Cell line (production host): High Five / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P27427
#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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 6% v/v Ethylene glycol, 0.1 M Citric acid pH 3.5, 10% w/v Polyethylene glycol 6.000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97845 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 59514 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.492
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.4 % / Rmerge(I) obs: 2.113 / Mean I/σ(I) obs: 1.078 / Num. unique obs: 5937 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.497→34.935 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 36.5
RfactorNum. reflection% reflection
Rfree0.2571 2170 5.04 %
Rwork0.231 --
obs0.2311 43023 72.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.497→34.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9336 0 56 201 9593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039657
X-RAY DIFFRACTIONf_angle_d0.70613120
X-RAY DIFFRACTIONf_dihedral_angle_d14.8245744
X-RAY DIFFRACTIONf_chiral_restr0.0431436
X-RAY DIFFRACTIONf_plane_restr0.0051651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4967-2.55470.4118400.3331861X-RAY DIFFRACTION23
2.5547-2.61860.418530.2791997X-RAY DIFFRACTION26
2.6186-2.68940.3233520.27581200X-RAY DIFFRACTION31
2.6894-2.76850.3254890.27111347X-RAY DIFFRACTION36
2.7685-2.85780.27321100.27921658X-RAY DIFFRACTION45
2.8578-2.95990.35341160.29032029X-RAY DIFFRACTION54
2.9599-3.07830.40661340.27442639X-RAY DIFFRACTION70
3.0783-3.21830.2831900.26863746X-RAY DIFFRACTION99
3.2183-3.38790.31151970.25363716X-RAY DIFFRACTION100
3.3879-3.59990.28062270.24913792X-RAY DIFFRACTION100
3.5999-3.87760.30711840.22873770X-RAY DIFFRACTION100
3.8776-4.26720.28711880.22943800X-RAY DIFFRACTION100
4.2672-4.88320.24552080.21323760X-RAY DIFFRACTION100
4.8832-6.14690.27032020.26223763X-RAY DIFFRACTION100
6.1469-34.93870.33881800.2913775X-RAY DIFFRACTION100
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)
10.0894-0.05920.32770.27510.14220.8293-0.09920.0487-0.03330.03230.0677-0.0371-0.49450.5014-0.28890.2172-0.266-0.05640.3340.02940.180512.6965.3046-13.8709
20.41250.0568-0.09590.07060.09891.6885-0.25930.084-0.0547-0.07650.0544-0.174-0.16740.6636-0.7145-0.0067-0.1489-0.04260.3075-0.04070.206619.7810.08420.9897
30.14680.04560.08780.1718-0.43531.295-0.1655-0.10550.05860.30680.15030.0538-0.3442-0.0207-0.0277-0.103-0.18450.0159-0.0131-0.02840.0978-0.48834.548629.9803
41.95930.4565-1.08122.382-0.5562.285-0.05040.4113-0.0964-0.20550.0075-0.09970.120.34680.21640.35310.11890.1380.5325-0.05690.265968.666125.3397-34.4541
50.27540.0950.41290.1690.16070.5919-0.127-0.4147-0.14690.2011-0.06480.17560.3183-0.7447-0.11640.1013-0.31570.0280.247-0.00840.111939.600418.048934.9383
60.1431-0.0237-0.00140.13980.2350.36350.11350.0355-0.04850.09190.01240.03450.18340.0848-0.2793-0.0030.0872-0.0260.0367-0.0170.184656.135627.0275-4.2165
70.095-0.02230.34510.0829-0.13812.24950.032-0.0390.0457-0.0398-0.0080.0424-0.4208-0.74390.14780.30030.02010.01150.2302-0.02610.200544.837432.7075-5.5749
81.09140.43190.69811.4555-0.32441.05-0.37390.73880.1373-0.38630.1017-0.05290.4561-0.1921-0.00240.5881-0.3292-0.07920.86410.11040.721840.1705-39.8696-104.9029
90.19770.1082-0.33670.4882-0.77511.3398-0.1141-0.17530.15990.237-0.3096-0.2592-1.61470.2583-0.1681.40030.0516-0.12850.6217-0.06260.878552.4431-11.8384-25.5615
100.0867-0.09020.24160.1643-0.6392.76220.0508-0.1706-0.0567-0.1218-0.0596-0.1178-0.822-0.1680.03191.1422-0.1785-0.11860.6150.02620.767858.5394-14.2263-14.8927
110.6490.0018-0.47961.6949-0.65680.6079-0.2218-0.31070.31960.2764-0.1256-0.29-1.0475-0.14110.14981.28240.2761-0.06980.60320.03610.926344.3006-10.1319-43.0807
120.07110.0004-0.33350.03470.03951.7931-0.12390.26640.3454-0.1334-0.3513-0.1791-0.28470.4030.16011.5577-0.1717-0.0970.8099-0.0030.988145.1883-8.1691-65.2019
134.57710.6693-0.3811.971-0.39540.9141-0.08980.2650.17680.1605-0.3186-0.0131-0.6434-0.84480.11150.66350.1141-0.01210.66730.06710.772439.7173-18.9374-69.4828
140.60210.07990.38270.01110.04970.24050.07970.10520.1764-0.04840.13720.2007-0.3427-0.420.29820.63060.3311-0.17840.66880.0381.092738.3476-17.3085-58.2163
150.89360.1630.39470.1650.25511.7414-0.08380.27990.0379-0.0294-0.1854-0.166-0.21120.1609-0.00170.5201-0.10280.00020.3542-0.00710.725357.5001-30.2913-92.9063
161.26460.40580.00751.20050.55781.04440.3138-0.0716-0.0033-0.8234-0.0543-0.106-0.11170.37070.04060.9147-0.139-0.13750.51090.13540.850457.7512-23.3028-26.5928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 310 )
3X-RAY DIFFRACTION3chain 'A' and (resid 311 through 472 )
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 44 )
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 287 )
6X-RAY DIFFRACTION6chain 'B' and (resid 288 through 354 )
7X-RAY DIFFRACTION7chain 'B' and (resid 355 through 472 )
8X-RAY DIFFRACTION8chain 'C' and (resid 25 through 45 )
9X-RAY DIFFRACTION9chain 'C' and (resid 46 through 129 )
10X-RAY DIFFRACTION10chain 'C' and (resid 130 through 168 )
11X-RAY DIFFRACTION11chain 'C' and (resid 169 through 212 )
12X-RAY DIFFRACTION12chain 'C' and (resid 213 through 231 )
13X-RAY DIFFRACTION13chain 'C' and (resid 232 through 277 )
14X-RAY DIFFRACTION14chain 'C' and (resid 278 through 310 )
15X-RAY DIFFRACTION15chain 'C' and (resid 311 through 448 )
16X-RAY DIFFRACTION16chain 'C' and (resid 449 through 472 )

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