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- PDB-6p7s: Crystal Structure of the Cedar henipavirus Attachment G Glycoprot... -

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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 / exo-alpha-sialidase activity / embryonic pattern specification / neural crest cell migration / ephrin receptor signaling pathway ...Ephrin signaling / EPH-Ephrin signaling / : / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / presynapse assembly / exo-alpha-sialidase activity / embryonic pattern specification / neural crest cell migration / ephrin receptor signaling pathway / positive regulation of T cell proliferation / T cell costimulation / ephrin receptor binding / axon guidance / nervous system development / host cell surface receptor binding / symbiont entry into host cell / membrane raft / viral envelope / glutamatergic synapse / synapse / virion attachment to host cell / host cell plasma membrane / virion membrane / nucleus / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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-Acetylglucosamine


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

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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: 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

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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

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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

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