[English] 日本語
Yorodumi
- PDB-6p7s: Crystal Structure of the Cedar henipavirus Attachment G Glycoprot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p7s
TitleCrystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in complex with the receptor ephrin-B1
Components
  • Attachment glycoprotein
  • Ephrin-B1
KeywordsVIRAL PROTEIN / Cedar virus / attachment / glycoprotein / G protein / receptor / ephrin-B1 / henipavirus
Function / homology
Function and homology information


Ephrin signaling / EPH-Ephrin signaling / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / presynapse assembly / embryonic pattern specification / regulation of autophagosome assembly / neural crest cell migration / exo-alpha-sialidase activity / ephrin receptor signaling pathway ...Ephrin signaling / EPH-Ephrin signaling / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / presynapse assembly / embryonic pattern specification / regulation of autophagosome assembly / neural crest cell migration / exo-alpha-sialidase activity / ephrin receptor signaling pathway / T cell proliferation / ephrin receptor binding / T cell costimulation / positive regulation of T cell proliferation / axon guidance / nervous system development / presynaptic membrane / host cell surface receptor binding / membrane raft / viral envelope / synapse / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / glutamatergic synapse / virion membrane / cell surface / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase ...Ephrin-B ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Attachment glycoprotein / Ephrin-B1
Similarity search - Component
Biological speciesCedar virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsXu, K. / Nikolov, D.B. / Xu, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural and functional analyses reveal promiscuous and species specific use of ephrin receptors by Cedar virus.
Authors: Laing, E.D. / Navaratnarajah, C.K. / Cheliout Da Silva, S. / Petzing, S.R. / Xu, Y. / Sterling, S.L. / Marsh, G.A. / Wang, L.F. / Amaya, M. / Nikolov, D.B. / Cattaneo, R. / Broder, C.C. / Xu, K.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.1Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Attachment glycoprotein
B: Ephrin-B1
C: Attachment glycoprotein
D: Ephrin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,77916
Polymers130,1494
Non-polymers3,62912
Water00
1
A: Attachment glycoprotein
B: Ephrin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1748
Polymers65,0752
Non-polymers2,0996
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint19 kcal/mol
Surface area23700 Å2
MethodPISA
2
C: Attachment glycoprotein
D: Ephrin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6058
Polymers65,0752
Non-polymers1,5306
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint20 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.570, 207.570, 119.377
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA208 - 5623
211chain CC208 - 5621
112chain BB29 - 1392
212chain DD30 - 1391

NCS ensembles :
ID
1
2

-
Components

#1: Protein Attachment glycoprotein


Mass: 48955.164 Da / Num. of mol.: 2 / Fragment: globular domain (UNP residues 193-622)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cedar virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: J7H333
#2: Protein Ephrin-B1 / CEK5 receptor ligand / CEK5-L / EFL-3 / ELK ligand / ELK-L / EPH-related receptor tyrosine kinase ...CEK5 receptor ligand / CEK5-L / EFL-3 / ELK ligand / ELK-L / EPH-related receptor tyrosine kinase ligand 2 / LERK-2 / Stimulated by retinoic acid gene 1 protein


Mass: 16119.517 Da / Num. of mol.: 2 / Fragment: UNP residues 29-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Efnb1, Epl2, Eplg2, Lerk2, Stra1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P52795
#3: 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
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 8
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.7 Å3/Da / Density % sol: 78.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris, pH 8.5, 20% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9192 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 10, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9192 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 37299 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 132.64 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.061 / Rrim(I) all: 0.158 / Χ2: 1.248 / Net I/σ(I): 5 / Num. measured all: 414726
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.5-3.6311.136910.5070.6710.791100
3.63-3.7711.137130.6760.4060.872100
3.77-3.9411.237260.810.3410.86100
3.94-4.1511.236970.9010.2260.9461000.7340.769
4.15-4.4111.237270.9530.1341.141000.4380.459
4.41-4.7511.337220.9760.0841.3981000.2720.285
4.75-5.2311.237150.9840.0631.571000.2050.215
5.23-5.9811.237420.9830.0591.5611000.1890.198
5.98-7.531137480.9910.0451.5831000.1450.152
7.53-5010.738180.9970.0261.75499.90.0820.086

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→44.94 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.56
RfactorNum. reflection% reflection
Rfree0.2275 2007 5.39 %
Rwork0.1959 --
obs0.1976 37244 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.93 Å2 / Biso mean: 49.91 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: final / Resolution: 3.49→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8879 0 235 0 9114
Biso mean--71.44 --
Num. residues----1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119371
X-RAY DIFFRACTIONf_angle_d1.52212689
X-RAY DIFFRACTIONf_chiral_restr0.0661414
X-RAY DIFFRACTIONf_plane_restr0.0091597
X-RAY DIFFRACTIONf_dihedral_angle_d19.193480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3720X-RAY DIFFRACTION17.579TORSIONAL
12C3720X-RAY DIFFRACTION17.579TORSIONAL
21B1183X-RAY DIFFRACTION17.579TORSIONAL
22D1183X-RAY DIFFRACTION17.579TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.49-3.57720.37621390.33932428256796
3.5772-3.67390.32361400.298524982638100
3.6739-3.78190.32421420.263925032645100
3.7819-3.90390.28611470.249825242671100
3.9039-4.04340.26881440.236624972641100
4.0434-4.20520.25831460.226225182664100
4.2052-4.39640.22531440.199925132657100
4.3964-4.6280.22481420.172125142656100
4.628-4.91760.20021440.152825202664100
4.9176-5.29670.18431440.158125232667100
5.2967-5.82870.19171450.162225442689100
5.8287-6.66980.27041440.18225322676100
6.6698-8.39430.23341430.197625402683100
8.3943-44.94390.18871430.18922583272699

+
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://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