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- PDB-1g5g: FRAGMENT OF FUSION PROTEIN FROM NEWCASTLE DISEASE VIRUS -

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Basic information

Entry
Database: PDB / ID: 1g5g
TitleFRAGMENT OF FUSION PROTEIN FROM NEWCASTLE DISEASE VIRUS
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / fusion protein / NDV / Newcastle disease virus / paramyxovirus
Function / homology
Function and homology information


membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #2480 / Head and neck region of the ectodomain of NDV fusion glycoprotein / Newcastle disease virus like domain / Head and neck region of the ectodomain of NDV fusion glycoprotein / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix Hairpins / Immunoglobulin-like / Beta Barrel / Sandwich ...Helix Hairpins - #2480 / Head and neck region of the ectodomain of NDV fusion glycoprotein / Newcastle disease virus like domain / Head and neck region of the ectodomain of NDV fusion glycoprotein / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix Hairpins / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesAvian orthoavulavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, phase extension / Resolution: 3.3 Å
AuthorsLawrence, M.C. / Smith, B.J.
CitationJournal: Structure / Year: 2001
Title: The structure of the fusion glycoprotein of Newcastle disease virus suggests a novel paradigm for the molecular mechanism of membrane fusion.
Authors: Chen, L. / Gorman, J.J. / McKimm-Breschkin, J. / Lawrence, L.J. / Tulloch, P.A. / Smith, B.J. / Colman, P.M. / Lawrence, M.C.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end

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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)310,96318
Polymers306,5216
Non-polymers4,44212
Water0
1
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,7669
Polymers153,2613
Non-polymers2,5056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25830 Å2
ΔGint-88 kcal/mol
Surface area43770 Å2
MethodPISA
2
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,1979
Polymers153,2613
Non-polymers1,9376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25070 Å2
ΔGint-101 kcal/mol
Surface area43580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.39, 308.33, 243.00
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Fusion glycoprotein F0


Mass: 51086.871 Da / Num. of mol.: 6
Fragment: FULL-LENGTH ECTODOMAIN (RESIDUES L32-R501) FOLLOWED BY C-MYC PURIFICATION TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian orthoavulavirus 1 / Genus: Avulavirus
Strain: Newcastle disease virus strain Queensland/66, V4 ISOLATE
References: UniProt: A9LSB1, UniProt: P35936*PLUS
#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.: 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
#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.: 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
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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: 15

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.170.04
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6.5ammonium sulphate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
2932vapor diffusion, hanging drop8.5Tris HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Method: unknown / Details: unpublished data

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11081
21081
32771
42771
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODEMACSCIENCE11.54181.5418
ROTATING ANODEMACSCIENCE21.54181.5418
SYNCHROTRONAPS 14-BM-C31.0371.037
SYNCHROTRONAPS 14-BM-D411
Detector
TypeIDDetectorDate
RIGAKU RAXIS II1IMAGE PLATE1999
RIGAKU RAXIS IV2IMAGE PLATE1999
ADSC QUANTUM 43CCD1999
ADSC QUANTUM 44CCD1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.0371
311
ReflectionResolution: 3.3→25 Å / Num. all: 76017 / Num. obs: 73130 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 7.04
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.812 / Num. unique all: 7502 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 438164
Reflection shell
*PLUS
% possible obs: 87.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: SIR, phase extension / Resolution: 3.3→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 3359 RANDOM
Rwork0.224 --
all-70418 -
obs-65746 -
Refinement stepCycle: LAST / Resolution: 3.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16050 0 291 0 16341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.5

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