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- PDB-6thg: Cedar Virus attachment glycoprotein (G) in complex with human eph... -

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Basic information

Entry
Database: PDB / ID: 6thg
TitleCedar Virus attachment glycoprotein (G) in complex with human ephrin-B1
Components
  • Attachment glycoprotein
  • Ephrin-B1
KeywordsVIRAL PROTEIN / attachment glycoprotein / beta-propeller / ephrin-B1 / complex
Function / homology
Function and homology information


exo-alpha-sialidase activity / embryonic pattern specification / regulation of autophagosome assembly / EPH-Ephrin signaling / Ephrin signaling / neural crest cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / T cell proliferation / positive regulation of T cell proliferation ...exo-alpha-sialidase activity / embryonic pattern specification / regulation of autophagosome assembly / EPH-Ephrin signaling / Ephrin signaling / neural crest cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / axon guidance / cell-cell signaling / presynaptic membrane / cell adhesion / 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 / cell surface / extracellular exosome / 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 / Cupredoxin
Similarity search - Domain/homology
Attachment glycoprotein / Attachment glycoprotein / Ephrin-B1
Similarity search - Component
Biological speciesCedar virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.074 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 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 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 2.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 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
B: Attachment glycoprotein
D: Ephrin-B1
A: Attachment glycoprotein
E: Attachment glycoprotein
G: Attachment glycoprotein
I: Attachment glycoprotein
C: Ephrin-B1
F: Ephrin-B1
H: Ephrin-B1
J: Ephrin-B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,59940
Polymers330,34810
Non-polymers10,25130
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The ephrin-B1 complex with CedV-G is stable on SEC and is validated by cellular binding assays.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.796, 138.435, 235.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 211 through 633)
21(chain B and resid 211 through 629)
31(chain E and resid 211 through 629)
41(chain G and resid 211 through 633)
51(chain I and resid 211 through 633)
12(chain C and resid 31 through 164)
22(chain D and (resid 31 through 65 or (resid 66...
32(chain F and resid 31 through 164)
42(chain H and resid 31 through 164)
52(chain J and resid 31 through 164)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 211 through 633)A211 - 633
211(chain B and resid 211 through 629)B211 - 629
311(chain E and resid 211 through 629)E211 - 629
411(chain G and resid 211 through 633)G211 - 633
511(chain I and resid 211 through 633)I211 - 633
112(chain C and resid 31 through 164)C31 - 164
212(chain D and (resid 31 through 65 or (resid 66...D31 - 65
222(chain D and (resid 31 through 65 or (resid 66...D66 - 67
232(chain D and (resid 31 through 65 or (resid 66...D31 - 171
242(chain D and (resid 31 through 65 or (resid 66...D31 - 171
252(chain D and (resid 31 through 65 or (resid 66...D31 - 171
262(chain D and (resid 31 through 65 or (resid 66...D31 - 171
312(chain F and resid 31 through 164)F31 - 164
412(chain H and resid 31 through 164)H31 - 164
512(chain J and resid 31 through 164)J31 - 164

NCS ensembles :
ID
1
2

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Components

#1: Protein
Attachment glycoprotein


Mass: 48820.957 Da / Num. of mol.: 5
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: Protein
Ephrin-B1 / EFL-3 / ELK ligand / ELK-L / EPH-related receptor tyrosine kinase ligand 2 / LERK-2


Mass: 17248.686 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNB1, EFL3, EPLG2, LERK2 / Plasmid: pHL-sec / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P98172
#3: 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.: 6
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
#4: 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.: 7
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
#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.: 17
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
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

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% polyethylene glycol 1500 (w/v), 0.1 M PCB (sodium propionate, sodium cacodylate, and BIS-TRIS propane) pH 5.0, and 0.02 M cadmium chloride dihydrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 4.07→70.17 Å / Num. obs: 30120 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 122.57 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.407 / Rpim(I) all: 0.173 / Net I/σ(I): 3.4
Reflection shellResolution: 4.07→4.14 Å / Rmerge(I) obs: 2.192 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1373 / CC1/2: 0.359 / Rpim(I) all: 0.914 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6THB

6thb


Resolution: 4.074→69.218 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.39
RfactorNum. reflection% reflection
Rfree0.3141 1473 4.9 %
Rwork0.2759 --
obs0.2778 30051 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 385.92 Å2 / Biso mean: 152.7932 Å2 / Biso min: 79.26 Å2
Refinement stepCycle: final / Resolution: 4.074→69.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22104 0 668 0 22772
Biso mean--175.38 --
Num. residues----2763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10416X-RAY DIFFRACTION8.439TORSIONAL
12B10416X-RAY DIFFRACTION8.439TORSIONAL
13E10416X-RAY DIFFRACTION8.439TORSIONAL
14G10416X-RAY DIFFRACTION8.439TORSIONAL
15I10416X-RAY DIFFRACTION8.439TORSIONAL
21C3355X-RAY DIFFRACTION8.439TORSIONAL
22D3355X-RAY DIFFRACTION8.439TORSIONAL
23F3355X-RAY DIFFRACTION8.439TORSIONAL
24H3355X-RAY DIFFRACTION8.439TORSIONAL
25J3355X-RAY DIFFRACTION8.439TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.0745-4.2060.39241290.3542245696
4.206-4.35630.351220.33122587100
4.3563-4.53070.32621440.32548100
4.5307-4.73680.28631450.27722553100
4.7368-4.98650.29911470.26442558100
4.9865-5.29880.30941220.26712589100
5.2988-5.70780.34341440.28032594100
5.7078-6.28180.31021340.27912628100
6.2818-7.190.33181250.27752613100
7.19-9.05540.29951330.27062660100
9.0554-69.2180.29491280.2442792100
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)
10.29250.3017-0.65823.021-1.04434.34070.143-0.0676-0.4180.2219-0.2067-0.11430.0170.23570.0360.5279-0.1168-0.11920.96050.0921.4418-48.2811-48.136334.7248
22.38932.6844-1.58474.48431.17088.5025-0.05530.6916-0.3471-0.08680.21640.2295-0.0933-0.9118-0.18690.524-0.084-0.15461.27490.01791.5945-75.5597-52.797520.7184
33.28720.69080.32294.1925-0.14371.92510.06620.1545-0.235-0.1855-0.21480.04340.26080.25440.15540.55320.09160.02791.3180.05571.6554-60.0465-23.122-8.3886
41.03020.01760.82042.0361-0.29044.86010.13180.0920.0164-0.02970.06630.1326-0.4786-0.3785-0.15870.76970.1482-0.04110.8057-0.0881.2022-37.923121.02738.4345
51.44640.92.03312.35210.83822.14610.20210.11280.13441.98990.5061-1.00571.56691.6528-0.38662.35410.7666-0.61891.8239-0.34541.6208-4.177-20.671656.3673
61.43870.89731.29586.75744.81913.90020.44470.3615-0.2436-3.00340.5938-1.8896-2.1681-0.406-0.32642.30110.18520.86251.0624-0.11311.5472-32.55620.7226-12.6751
74.71531.22082.24412.9303-0.24774.29061.0149-0.91241.9641.1858-0.30860.3107-1.2389-0.3556-0.64620.89520.09510.40151.2496-0.1211.762-75.0136-15.934817.6637
81.5054-1.0484-2.00683.5373-2.30755.28770.1715-0.08820.35220.51850.2701-0.8681-0.88530.4606-0.38580.7399-0.2950.1341.2563-0.23361.7115-7.412816.100639.3273
95.6738-1.5414-2.12446.4815-1.17768.7883-0.1357-0.1567-0.1092-0.67660.3228-0.01230.24570.9071-0.18571.0536-0.1823-0.19240.9524-0.08990.9065-21.8787-14.195331.9271
102.3311-3.42520.04824.2016-0.07382.38060.611-0.0854-0.0846-0.612-0.842-0.61480.24950.0622-0.04971.7668-0.49790.76451.7648-0.19042.1284-3.648813.53-22.7685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 207 through 625)B207 - 625
2X-RAY DIFFRACTION2(chain 'D' and resid 32 through 166)D32 - 166
3X-RAY DIFFRACTION3(chain 'A' and resid 208 through 625)A208 - 625
4X-RAY DIFFRACTION4(chain 'E' and resid 211 through 640)E211 - 640
5X-RAY DIFFRACTION5(chain 'G' and resid 211 through 625)G211 - 625
6X-RAY DIFFRACTION6(chain 'I' and resid 209 through 625)I210 - 625
7X-RAY DIFFRACTION7(chain 'C' and resid 31 through 167)C31 - 167
8X-RAY DIFFRACTION8(chain 'F' and resid 31 through 167)F31 - 167
9X-RAY DIFFRACTION9(chain 'H' and resid 31 through 164)H31 - 164
10X-RAY DIFFRACTION10(chain 'J' and resid 31 through 166)J31 - 166

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