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- PDB-5evm: Crystal Structure of Nipah Virus Fusion Glycoprotein in the Prefu... -

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Basic information

Entry
Database: PDB / ID: 5evm
TitleCrystal Structure of Nipah Virus Fusion Glycoprotein in the Prefusion State
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / fusion protein / Nipah / prefusion / paramyxovirus / henipavirus
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
MALONATE ION / Fusion glycoprotein F0
Similarity search - Component
Biological speciesNipah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.367 Å
AuthorsXu, K. / Nikolov, D.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI054715 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI077995 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS38586 United States
CitationJournal: Plos Pathog. / Year: 2015
Title: Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly.
Authors: Xu, K. / Chan, Y.P. / Bradel-Tretheway, B. / Akyol-Ataman, Z. / Zhu, Y. / Dutta, S. / Yan, L. / Feng, Y. / Wang, L.F. / Skiniotis, G. / Lee, B. / Zhou, Z.H. / Broder, C.C. / Aguilar, H.C. / Nikolov, D.B.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 11, 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 / 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 / _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_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,58730
Polymers350,4446
Non-polymers12,14324
Water0
1
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,29315
Polymers175,2223
Non-polymers6,07112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24270 Å2
ΔGint-11 kcal/mol
Surface area56570 Å2
MethodPISA
2
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,29315
Polymers175,2223
Non-polymers6,07112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24090 Å2
ΔGint-8 kcal/mol
Surface area57080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)355.750, 355.750, 168.859
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein / Non-polymers , 2 types, 12 molecules ABCDEF

#1: Protein
Fusion glycoprotein F0 / Protein F


Mass: 58407.285 Da / Num. of mol.: 6 / Mutation: N67D, N305D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Cell (production host): Epithelia / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q9IH63
#9: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4

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Sugars , 7 types, 18 molecules

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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c2-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 5
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
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c2-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.87 Å3/Da / Density % sol: 79.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M HEPES, 1% Jeffamine ED-2001, 1.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 112890 / Num. obs: 112120 / % possible obs: 99.36 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 2.41
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 2.41 / % possible all: 93.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B9B

2b9b


Resolution: 3.367→43.158 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 5592 4.99 %
Rwork0.2133 --
obs0.2136 112057 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.367→43.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20802 0 810 0 21612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121928
X-RAY DIFFRACTIONf_angle_d1.52129759
X-RAY DIFFRACTIONf_dihedral_angle_d17.2048141
X-RAY DIFFRACTIONf_chiral_restr0.0913766
X-RAY DIFFRACTIONf_plane_restr0.0263683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3669-3.40520.4341700.40472947X-RAY DIFFRACTION83
3.4052-3.44520.36631810.39333601X-RAY DIFFRACTION99
3.4452-3.48720.36611570.39183571X-RAY DIFFRACTION100
3.4872-3.53130.37081600.38433583X-RAY DIFFRACTION100
3.5313-3.57780.37862090.36393543X-RAY DIFFRACTION100
3.5778-3.62680.36981960.35653549X-RAY DIFFRACTION100
3.6268-3.67860.36312110.33863601X-RAY DIFFRACTION100
3.6786-3.73340.33581680.33933556X-RAY DIFFRACTION100
3.7334-3.79170.31231730.31543588X-RAY DIFFRACTION100
3.7917-3.85390.30761810.30033564X-RAY DIFFRACTION100
3.8539-3.92030.31342310.28763542X-RAY DIFFRACTION100
3.9203-3.99150.27631810.27823578X-RAY DIFFRACTION100
3.9915-4.06820.26041740.26213554X-RAY DIFFRACTION100
4.0682-4.15120.28672040.25143593X-RAY DIFFRACTION100
4.1512-4.24140.22681900.24333561X-RAY DIFFRACTION100
4.2414-4.340.23791980.23633590X-RAY DIFFRACTION100
4.34-4.44840.22081750.22263576X-RAY DIFFRACTION100
4.4484-4.56860.19171830.19443559X-RAY DIFFRACTION100
4.5686-4.70280.18361710.18633589X-RAY DIFFRACTION100
4.7028-4.85440.16272210.18083526X-RAY DIFFRACTION100
4.8544-5.02770.19251930.19013543X-RAY DIFFRACTION100
5.0277-5.22870.20141840.18433600X-RAY DIFFRACTION100
5.2287-5.46620.20081980.17533602X-RAY DIFFRACTION100
5.4662-5.75370.18131610.18953581X-RAY DIFFRACTION100
5.7537-6.11330.23111850.18123568X-RAY DIFFRACTION100
6.1133-6.58380.1852000.17743569X-RAY DIFFRACTION100
6.5838-7.24350.17261830.16793554X-RAY DIFFRACTION100
7.2435-8.28530.15931790.15783587X-RAY DIFFRACTION100
8.2853-10.41430.1361950.11673531X-RAY DIFFRACTION99
10.4143-43.16140.16691800.16423559X-RAY DIFFRACTION99

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