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- PDB-3maw: Structure of the Newcastle disease virus F protein in the post-fu... -

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Basic information

Entry
Database: PDB / ID: 3maw
TitleStructure of the Newcastle disease virus F protein in the post-fusion conformation
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Fusion protein / class I / paramyxovirus / glycoprotein
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
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 / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Fusion glycoprotein F0
Similarity search - Component
Biological speciesNewcastle disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJardetzky, T.S. / Wen, X.
CitationJournal: Virology / Year: 2010
Title: Structure of the Newcastle disease virus F protein in the post-fusion conformation.
Authors: Swanson, K. / Wen, X. / Leser, G.P. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4708
Polymers102,3302
Non-polymers2,1406
Water00
1
A: Fusion glycoprotein F0
hetero molecules

A: Fusion glycoprotein F0
hetero molecules

A: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,70512
Polymers153,4953
Non-polymers3,2109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area35970 Å2
ΔGint-191 kcal/mol
Surface area53200 Å2
MethodPISA
2
B: Fusion glycoprotein F0
hetero molecules

B: Fusion glycoprotein F0
hetero molecules

B: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,70512
Polymers153,4953
Non-polymers3,2109
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area36170 Å2
ΔGint-187 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.253, 83.253, 461.406
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 34:102 or resseq 145:493 )
211chain B and (resseq 34:102 or resseq 145:493 )

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Components

#1: Protein Fusion glycoprotein F0 / Fusion glycoprotein F2 / Fusion glycoprotein F1


Mass: 51164.852 Da / Num. of mol.: 2 / Fragment: UNP RESIDUE 32-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Newcastle disease virus / Strain: Chicken/Australia-Victoria/32 / Gene: F / References: UniProt: P12572
#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: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
Sequence detailsH66L, I162N CONFLICT IN UNP ENTRY P12572

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% (wt/vol) polyethylene glycol 1000, 1.26 M ammonia sulfate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 14966 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 %
Reflection shellResolution: 3.5→3.63 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→48.65 Å / SU ML: 0.64 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 1004 6.73 %Random
Rwork0.2606 ---
obs0.2628 14925 99.83 %-
all-14973 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.158 Å2 / ksol: 0.3 e/Å3
Refinement stepCycle: LAST / Resolution: 3.5→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 140 0 6184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026274
X-RAY DIFFRACTIONf_angle_d0.4248576
X-RAY DIFFRACTIONf_dihedral_angle_d13.7112210
X-RAY DIFFRACTIONf_chiral_restr0.0261110
X-RAY DIFFRACTIONf_plane_restr0.0021094
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3022X-RAY DIFFRACTIONPOSITIONAL
12B3022X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.690.31141430.29511981X-RAY DIFFRACTION100
3.69-3.92080.36391420.29191980X-RAY DIFFRACTION100
3.9208-4.22280.27331530.24022000X-RAY DIFFRACTION100
4.2228-4.64640.2611660.19931993X-RAY DIFFRACTION100
4.6464-5.31570.25051360.20061968X-RAY DIFFRACTION100
5.3157-6.68570.31221240.27712009X-RAY DIFFRACTION100
6.6857-30.57060.27061400.25381990X-RAY DIFFRACTION99

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