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- PDB-3rrt: Structure of the RSV F protein in the post-fusion conformation -

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Basic information

Entry
Database: PDB / ID: 3rrt
TitleStructure of the RSV F protein in the post-fusion conformation
Components(Fusion glycoprotein F0) x 2
KeywordsVIRAL PROTEIN / six-helix bundle / membrane fusion
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1160 / Rhinovirus 14, subunit 4 - #50 / Rhinovirus 14, subunit 4 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Other non-globular / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMcLellan, J.S. / Yongping, Y. / Graham, B.S. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2011
Title: Structure of respiratory syncytial virus fusion glycoprotein in the postfusion conformation reveals preservation of neutralizing epitopes.
Authors: McLellan, J.S. / Yang, Y. / Graham, B.S. / Kwong, P.D.
History
DepositionApr 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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


Theoretical massNumber of molelcules
Total (without water)152,5596
Polymers152,5596
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53270 Å2
ΔGint-393 kcal/mol
Surface area52250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.024, 81.877, 271.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion glycoprotein F0


Mass: 9529.798 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Strain: A2 / Gene: fusion (F) protein / Plasmid: paH / Cell line (production host): HEK293F / Production host: homo sapiens (human) / References: UniProt: Q84850, UniProt: P03420*PLUS
#2: Protein Fusion glycoprotein F0


Mass: 41323.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Strain: A2 / Gene: fusion (F) protein / Plasmid: paH / Cell line (production host): HEK293F / Production host: homo sapiens (human) / References: UniProt: Q84850, UniProt: P03420*PLUS
Sequence details1) THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A VIRAL STRAIN NOT PRESENT IN THE DATABASE UNP ENTRY ...1) THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A VIRAL STRAIN NOT PRESENT IN THE DATABASE UNP ENTRY Q84850_HRSV. 2) THE FULL SEQUENCE PRESENT IN THE PLASMID WAS CLEAVED DURING EXPRESSION.

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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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 23% (w/v) PEG 3000, 0.1 M acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26109 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.208 / Rsym value: 0.208 / Net I/σ(I): 6.07
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7 / % possible all: 82.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RRR

3rrr


Resolution: 3.2→46.17 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 1331 5.13 %
Rwork0.253 --
obs0.255 25928 91.5 %
all-28339 -
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.74 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--23.3349 Å20 Å20 Å2
2--23.0759 Å20 Å2
3---0.259 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10064 0 0 0 10064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810223
X-RAY DIFFRACTIONf_angle_d1.0913817
X-RAY DIFFRACTIONf_dihedral_angle_d14.3263791
X-RAY DIFFRACTIONf_chiral_restr0.0571674
X-RAY DIFFRACTIONf_plane_restr0.0041734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1494-3.26190.394750.34721727X-RAY DIFFRACTION65
3.2619-3.39250.33371160.3092247X-RAY DIFFRACTION85
3.3925-3.54680.3361130.29652343X-RAY DIFFRACTION88
3.5468-3.73370.30351240.28032518X-RAY DIFFRACTION94
3.7337-3.96760.32361360.27162527X-RAY DIFFRACTION96
3.9676-4.27370.29521580.2272566X-RAY DIFFRACTION97
4.2737-4.70340.21671570.19232623X-RAY DIFFRACTION98
4.7034-5.38310.28631440.21712639X-RAY DIFFRACTION98
5.3831-6.77870.27461400.24162681X-RAY DIFFRACTION98
6.7787-46.17560.25541680.272726X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.03530.016-0.05440.12380.07490.2127-0.0207-0.0702-0.0379-0.00090.04770.1038-0.10980.0236-0.02670.3118-0.0063-0.02220.4727-0.04620.4654-7.7972-20.966722.2837
20.02930.0522-0.10460.19410.28460.35360.0674-0.0393-0.012-0.088-0.15070.1368-0.1572-0.04690.04860.23520.0686-0.0480.12830.00930.2594-22.0307-22.214422.3986
30.0834-0.06190.05980.16620.24070.3883-0.1286-0.11340.04790.0014-0.03320.1712-0.03470.06780.13960.1423-0.06190.06120.2956-0.02970.2961-14.0705-30.639630.5954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A or CHAIN B
2X-RAY DIFFRACTION1CHAIN A or CHAIN B
3X-RAY DIFFRACTION2CHAIN C or CHAIN D
4X-RAY DIFFRACTION2CHAIN C or CHAIN D
5X-RAY DIFFRACTION3CHAIN E or CHAIN F
6X-RAY DIFFRACTION3CHAIN E or CHAIN F

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