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- PDB-5nop: Structure of Mojiang virus attachment glycoprotein -

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Basic information

Entry
Database: PDB / ID: 5nop
TitleStructure of Mojiang virus attachment glycoprotein
ComponentsAttachment glycoprotein
KeywordsVIRAL PROTEIN / paramyxovirus / henipavirus / viral attachment / virus entry / 6-bladed beta-propeller
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Attachment glycoprotein
Similarity search - Component
Biological speciesMojiang virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsRissanen, I.R. / Ahmed, A.A. / Beaty, S. / Azarm, K. / Hong, P. / Nambulli, S. / Duprex, P.W. / Lee, B. / Bowden, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Idiosyncratic Mojiang virus attachment glycoprotein directs a host-cell entry pathway distinct from genetically related henipaviruses.
Authors: Rissanen, I. / Ahmed, A.A. / Azarm, K. / Beaty, S. / Hong, P. / Nambulli, S. / Duprex, W.P. / Lee, B. / Bowden, T.A.
History
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment glycoprotein
B: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9028
Polymers104,6902
Non-polymers2136
Water16,934940
1
A: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4514
Polymers52,3451
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4514
Polymers52,3451
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.040, 102.310, 162.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 193 and (name O or name...
21(chain B and ((resid 193 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and ((resid 193 and (name O or name...AA19330
12THRTHRTYRTYR(chain A and ((resid 193 and (name O or name...AA175 - 60512 - 442
13THRTHRTYRTYR(chain A and ((resid 193 and (name O or name...AA175 - 60512 - 442
14THRTHRTYRTYR(chain A and ((resid 193 and (name O or name...AA175 - 60512 - 442
15THRTHRTYRTYR(chain A and ((resid 193 and (name O or name...AA175 - 60512 - 442
16THRTHRTYRTYR(chain A and ((resid 193 and (name O or name...AA175 - 60512 - 442
17THRTHRTYRTYR(chain A and ((resid 193 and (name O or name...AA175 - 60512 - 442
21ASPASPASPASP(chain B and ((resid 193 and (name N or name...BB19330
22THRTHRGLYGLY(chain B and ((resid 193 and (name N or name...BB176 - 61513 - 452
23THRTHRGLYGLY(chain B and ((resid 193 and (name N or name...BB176 - 61513 - 452
24THRTHRGLYGLY(chain B and ((resid 193 and (name N or name...BB176 - 61513 - 452
25THRTHRGLYGLY(chain B and ((resid 193 and (name N or name...BB176 - 61513 - 452
26THRTHRGLYGLY(chain B and ((resid 193 and (name N or name...BB176 - 61513 - 452
27THRTHRGLYGLY(chain B and ((resid 193 and (name N or name...BB176 - 61513 - 452

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Components

#1: Protein Attachment glycoprotein


Mass: 52344.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Synthetic gene / Source: (gene. exp.) Mojiang virus / Gene: G, MojVGP5 / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: W8TIR7
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 16.4% PEG 6000, 0.82 M lithium chloride, 0.082 M citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.94→49.33 Å / Num. obs: 74486 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 18.96 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.156 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.94-1.9950.821.90.657198.4
8.68-49.334.60.03630.40.999199.1

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Processing

Software
NameVersionClassification
xia20.3.6.3data reduction
xia20.3.6.3data scaling
PHENIXdev_2283phasing
PHENIXdev_2283refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VSM

2vsm


Resolution: 1.94→49.325 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2224 3627 4.89 %
Rwork0.1817 --
obs0.1837 74170 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.74 Å2 / Biso mean: 20.8617 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.94→49.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6669 0 6 940 7615
Biso mean--35.7 27.8 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066860
X-RAY DIFFRACTIONf_angle_d0.7829319
X-RAY DIFFRACTIONf_chiral_restr0.0561004
X-RAY DIFFRACTIONf_plane_restr0.0061198
X-RAY DIFFRACTIONf_dihedral_angle_d12.7294106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3701X-RAY DIFFRACTION5.124TORSIONAL
12B3701X-RAY DIFFRACTION5.124TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.96550.31671410.26842550269196
1.9655-1.99250.31751380.24952683282199
1.9925-2.02090.27521310.25326912822100
2.0209-2.05110.32681410.249626882829100
2.0511-2.08320.27321680.24126622830100
2.0832-2.11730.28431420.23326592801100
2.1173-2.15380.26431340.227927262860100
2.1538-2.1930.25021290.223226912820100
2.193-2.23520.28911260.224127172843100
2.2352-2.28080.28461230.225927232846100
2.2808-2.33040.26991410.20582692283399
2.3304-2.38460.26151360.20392627276398
2.3846-2.44420.23851550.19142661281699
2.4442-2.51030.23121220.2012739286199
2.5103-2.58420.2481660.201226772843100
2.5842-2.66760.26871380.191527062844100
2.6676-2.76290.22561370.180527432880100
2.7629-2.87350.22471530.183327022855100
2.8735-3.00430.27851330.17752732286599
3.0043-3.16270.19551160.16922721283799
3.1627-3.36080.18771470.162127312878100
3.3608-3.62020.18651460.155927382884100
3.6202-3.98430.18491450.143527602905100
3.9843-4.56050.14061320.12632788292099
4.5605-5.74440.17781520.13532776292899
5.7444-49.34120.18041350.17492960309599

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