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- PDB-6pd4: Crystal Structure of Hendra Virus Attachment G Glycoprotein -

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Basic information

Entry
Database: PDB / ID: 6pd4
TitleCrystal Structure of Hendra Virus Attachment G Glycoprotein
ComponentsAttachment glycoprotein
KeywordsVIRAL PROTEIN / Hendra virus / attachment / glycoprotein / G protein / receptor / ephrin-B2 / henipavirus
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Glycoprotein / Glycoprotein G
Similarity search - Component
Biological speciesHendra henipavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXu, K. / Nikolov, D.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NS38486 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI057168 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI054715 United States
Citation
Journal: PLoS ONE / Year: 2012
Title: New insights into the Hendra virus attachment and entry process from structures of the virus G glycoprotein and its complex with Ephrin-B2.
Authors: Xu, K. / Chan, Y.P. / Rajashankar, K.R. / Khetawat, D. / Yan, L. / Kolev, M.V. / Broder, C.C. / Nikolov, D.B.
#1: Journal: Glycobiology / Year: 2012
Title: Site occupancy and glycan compositional analysis of two soluble recombinant forms of the attachment glycoprotein of Hendra virus.
Authors: Colgrave, M.L. / Snelling, H.J. / Shiell, B.J. / Feng, Y.R. / Chan, Y.P. / Bossart, K.N. / Xu, K. / Nikolov, D.B. / Broder, C.C. / Michalski, W.P.
History
DepositionJun 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_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: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,00923
Polymers98,8622
Non-polymers5,14621
Water10,863603
1
A: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,89012
Polymers49,4311
Non-polymers2,45911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Attachment glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,11811
Polymers49,4311
Non-polymers2,68710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.152, 73.244, 109.132
Angle α, β, γ (deg.)90.000, 91.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 176 through 604 or resid 3061 through 4811 or resid 5293 through 5294))
21(chain B and (resid 176 through 604 or resid 4171 through 5292 or resid 5296 through 5297))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 176 through 604 or resid 3061 through 4811 or resid 5293 through 5294))A176 - 604
121(chain A and (resid 176 through 604 or resid 3061 through 4811 or resid 5293 through 5294))A3061 - 4811
131(chain A and (resid 176 through 604 or resid 3061 through 4811 or resid 5293 through 5294))A5293 - 5294
211(chain B and (resid 176 through 604 or resid 4171 through 5292 or resid 5296 through 5297))B176 - 604
221(chain B and (resid 176 through 604 or resid 4171 through 5292 or resid 5296 through 5297))B4171 - 5292
231(chain B and (resid 176 through 604 or resid 4171 through 5292 or resid 5296 through 5297))B5296 - 5297

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Attachment glycoprotein / Glycoprotein


Mass: 49431.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra henipavirus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: F4YH71, UniProt: O89343*PLUS

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Sugars , 4 types, 8 molecules

#2: 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.: 4
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
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-3-2/a3-b1_a4-c1_a6-f1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Non-polymers , 2 types, 616 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG2000MME and 130 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 51943 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Χ2: 0.942 / Net I/σ(I): 7.9 / Num. measured all: 169409
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.282.50.23746970.662188.6
2.28-2.372.70.21150100.641194
2.37-2.482.90.18150900.662196.5
2.48-2.6130.15951670.691197.5
2.61-2.773.10.13552150.71198.4
2.77-2.993.40.11952980.791199.5
2.99-3.293.70.10453200.9199.8
3.29-3.763.80.08253111.2021100
3.76-4.743.70.06553791.68199.9
4.74-403.70.04154560.962199.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.924 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 2619 5.05 %
Rwork0.1667 49285 -
obs0.1687 51904 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.72 Å2 / Biso mean: 32.5236 Å2 / Biso min: 12.25 Å2
Refinement stepCycle: final / Resolution: 2.2→36.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 323 603 7734
Biso mean--55.56 35.97 -
Num. residues----865
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4084X-RAY DIFFRACTION10.95TORSIONAL
12B4084X-RAY DIFFRACTION10.95TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.23140.26921000.20472008210876
2.2314-2.27430.26231370.20262385252290
2.2743-2.32070.26321300.19022444257492
2.3207-2.37120.25461480.1882535268395
2.3712-2.42630.20821380.18052571270996
2.4263-2.4870.20721240.18052572269697
2.487-2.55420.23561600.17642592275298
2.5542-2.62940.19931290.17782617274698
2.6294-2.71420.22651440.17182622276698
2.7142-2.81120.2411420.17942668281099
2.8112-2.92370.20261650.17482627279299
2.9237-3.05670.22051300.18132683281399
3.0567-3.21780.23471250.165626922817100
3.2178-3.41920.18571500.160326532803100
3.4192-3.6830.18491260.159227302856100
3.683-4.05320.18131730.148226662839100
4.0532-4.63880.17771190.135227172836100
4.6388-5.84060.17381140.151927422856100
5.8406-36.92880.22441650.187627612926100

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