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- PDB-4ccf: Structure of Respiratory Syncytial Virus F protein head domain -

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Basic information

Entry
Database: PDB / ID: 4ccf
TitleStructure of Respiratory Syncytial Virus F protein head domain
ComponentsFUSION GLYCOPROTEIN F0
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesRESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPeat, T.S.
CitationJournal: To be Published
Title: Structure of Respiratory Syncytial Virus F Protein Head Domain
Authors: Peat, T.S.
History
DepositionOct 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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
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)381,0669
Polymers380,7786
Non-polymers2883
Water64936
1
D: FUSION GLYCOPROTEIN F0
E: FUSION GLYCOPROTEIN F0
F: FUSION GLYCOPROTEIN F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,5815
Polymers190,3893
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-75.2 kcal/mol
Surface area34520 Å2
MethodPISA
2
A: FUSION GLYCOPROTEIN F0
B: FUSION GLYCOPROTEIN F0
C: FUSION GLYCOPROTEIN F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,4854
Polymers190,3893
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-31.8 kcal/mol
Surface area34490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.380, 133.501, 116.420
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FUSION GLYCOPROTEIN F0 / RSV F


Mass: 63462.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: THE PROTEIN WAS PROTEOLYZED BY CELLULAR PROTEASES SOMETIME DURING EXPRESSION OR PURIFICATION
Source: (natural) RESPIRATORY SYNCYTIAL VIRUS / References: UniProt: G8EJ09, UniProt: P03420*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN WAS PROTEOLYZED DURING EXPRESSION OR PURIFICATION, SO THE FULL SEQUENCE IS NOT SEEN.

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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: 3.05 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growDetails: 25% PEG 8000, 200 MM AMMONIUM SULFATE, 200 MM SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→43.1 Å / Num. obs: 53253 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RRR

3rrr


Resolution: 2.65→43.07 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.277 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 1.746 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24718 2763 5.2 %RANDOM
Rwork0.21456 ---
obs0.21629 50404 87.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.065 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-0.6 Å2
2--1.14 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.65→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12142 0 15 36 12193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212425
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212169
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.95516909
X-RAY DIFFRACTIONr_angle_other_deg1.133.00527385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41651562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23625.072489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.616152150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7751548
X-RAY DIFFRACTIONr_chiral_restr0.0750.22036
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213907
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022721
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0173.7566299
X-RAY DIFFRACTIONr_mcbond_other3.0143.7566298
X-RAY DIFFRACTIONr_mcangle_it4.9065.6157844
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4444.1026126
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 161 -
Rwork0.322 3560 -
obs--83.54 %

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