[English] 日本語
Yorodumi
- PDB-6thb: Receptor binding domain of the Cedar Virus attachment glycoprotein (G) -

+
Open data


ID or keywords:

Loading...

-
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 / symbiont entry into host cell / viral envelope / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more