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- PDB-6thb: Receptor binding domain of the Cedar Virus attachment glycoprotein (G) -

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Basic information

Entry
Database: PDB / ID: 6thb
TitleReceptor binding domain of the Cedar Virus attachment glycoprotein (G)
ComponentsAttachment glycoprotein
KeywordsVIRAL PROTEIN / Receptor-binding / attachment / glycoprotein / 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 / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Attachment glycoprotein / Attachment glycoprotein
Similarity search - Component
Biological speciesCedar virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsPryce, R. / Rissanen, I. / Harlos, K. / Bowden, T.
Funding support United Kingdom, United States, 6items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (United Kingdom)MR/S007555/1 United Kingdom
Wellcome Trust203141/Z/16Z United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123449 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI069317 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115226 United States
CitationJournal: Life Sci Alliance / Year: 2020
Title: A key region of molecular specificity orchestrates unique ephrin-B1 utilization by Cedar virus.
Authors: Pryce, R. / Azarm, K. / Rissanen, I. / Harlos, K. / Bowden, T.A. / Lee, B.
History
DepositionNov 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 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: Attachment glycoprotein
B: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,51815
Polymers97,6422
Non-polymers2,87613
Water1629
1
A: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3698
Polymers48,8211
Non-polymers1,5487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1487
Polymers48,8211
Non-polymers1,3276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)201.460, 201.460, 112.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Attachment glycoprotein


Mass: 48820.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cedar virus / Plasmid: pHL-sec / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: A0A185KRV2, UniProt: J7H333*PLUS
#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.: 13
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5% (w/v) polyethylene glycol 6000, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.78→58 Å / Num. obs: 65603 / % possible obs: 99.9 % / Redundancy: 20.5 % / Biso Wilson estimate: 69.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.037 / Net I/σ(I): 15.4
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 19.5 % / Rmerge(I) obs: 1.776 / Mean I/σ(I) obs: 2 / Num. unique obs: 4849 / CC1/2: 0.777 / Rpim(I) all: 0.412 / % possible all: 99.6

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VWD

2vwd


Resolution: 2.78→49.241 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.87
RfactorNum. reflection% reflection
Rfree0.2274 3272 4.99 %
Rwork0.2012 --
obs0.2025 65557 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.71 Å2 / Biso mean: 86.284 Å2 / Biso min: 31.88 Å2
Refinement stepCycle: final / Resolution: 2.78→49.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 182 9 6889
Biso mean--102.64 62.01 -
Num. residues----835
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7801-2.82160.37281450.35532695
2.8216-2.86570.35781440.32362669
2.8657-2.91260.29631480.28922701
2.9126-2.96290.31951280.27222727
2.9629-3.01670.29631430.27232644
3.0167-3.07470.30741360.2772716
3.0747-3.13750.25631380.27332675
3.1375-3.20570.27821820.26182704
3.2057-3.28030.24821440.26152644
3.2803-3.36230.34951390.25382709
3.3623-3.45320.29271420.24052693
3.4532-3.55470.24731390.22912724
3.5547-3.66950.29171420.22482690
3.6695-3.80060.24211600.20852692
3.8006-3.95270.21411250.20462725
3.9527-4.13250.19081490.18792706
4.1325-4.35020.2041630.16762691
4.3502-4.62260.18741310.14752732
4.6226-4.97920.15251500.13472690
4.9792-5.47970.16231300.15872744
5.4797-6.27120.20811300.17792753
6.2712-7.89580.18171310.19062748
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)
10.76210.8464-1.29613.9341-0.6442.5851-0.19290.09520.1411-0.42840.1346-0.4308-1.59460.97510.24621.4084-0.3649-0.20130.53420.14750.635695.7028-34.4556-20.9074
21.01630.1009-0.1281.16061.14784.758-0.22380.07180.05990.2145-0.09290.1662-0.4792-0.33620.21010.5032-0.0173-0.06480.33730.02950.454984.2687-49.8968-9.9106
31.90310.39590.40512.71050.20384.4757-0.20720.18730.2194-0.2464-0.059-0.0534-0.71360.03530.1620.5249-0.1281-0.05990.33990.02540.455786.678-49.9017-25.3497
40.2163-0.2641-0.20890.98570.69581.1578-0.19320.16540.2471-0.28360.1585-0.1413-1.46170.18510.44641.2621-0.3682-0.25270.49880.13950.541392.7896-38.2853-26.6827
53.4164-1.6361.14153.4376-2.98279.15230.1161-0.02250.3413-0.161-0.1652-0.54520.0490.73540.16020.8707-0.03370.14230.2810.07040.7502100.334418.0313-35.1241
68.8389-3.59194.25769.4058-4.81067.7270.3912-0.69650.5610.8751-0.3958-0.9652-0.04710.36750.01580.9095-0.037-0.0160.34970.03270.592100.215616.0597-20.6206
70.2652-0.26230.19163.6015-0.43282.28190.0526-0.1915-0.10330.35510.068-0.21351.28990.156-0.00031.55240.07950.0560.45890.06420.635797.4533-0.2541-20.0782
86.0411-1.2579-0.07426.3274-1.44281.88380.2953-0.5211-0.34010.60180.09711.09260.5663-0.4235-0.32491.9617-0.23560.20880.44120.12450.746187.4844-3.389-17.6628
90.41650.3770.42093.8947-1.59612.2040.19430.2049-0.2329-0.31780.0309-0.11251.95210.6280.3472.20050.24120.06360.05250.14510.6749100.4139-3.1604-36.042
104.5572-2.1907-0.94465.54564.84654.57450.12930.18340.6547-0.7831-0.222-0.70681.15811.4668-0.1411.13580.20840.28240.68310.18030.7552108.99819.83-42.1745
118.92490.47964.87265.6505-1.64434.10020.26480.17520.0246-0.3801-0.2264-0.22730.6590.37510.02840.79830.01130.21730.31990.02740.5597100.116317.5826-38.305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 209 through 285 )A209 - 285
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 428 )A286 - 428
3X-RAY DIFFRACTION3chain 'A' and (resid 429 through 588 )A429 - 588
4X-RAY DIFFRACTION4chain 'A' and (resid 589 through 625 )A589 - 625
5X-RAY DIFFRACTION5chain 'B' and (resid 208 through 250 )B208 - 250
6X-RAY DIFFRACTION6chain 'B' and (resid 251 through 280 )B251 - 280
7X-RAY DIFFRACTION7chain 'B' and (resid 281 through 428 )B281 - 428
8X-RAY DIFFRACTION8chain 'B' and (resid 429 through 451 )B429 - 451
9X-RAY DIFFRACTION9chain 'B' and (resid 452 through 547 )B452 - 547
10X-RAY DIFFRACTION10chain 'B' and (resid 548 through 581 )B548 - 581
11X-RAY DIFFRACTION11chain 'B' and (resid 582 through 625 )B582 - 625

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