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

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Basic information

Entry
Database: PDB / ID: 3rrr
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 / host cell Golgi membrane / 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 / 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: 2.821 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 1.3Apr 2, 2014Group: Source and taxonomy
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.5Sep 13, 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
G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
I: Fusion glycoprotein F0
L: Fusion glycoprotein F0
M: Fusion glycoprotein F0
N: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,77224
Polymers305,11812
Non-polymers2,65412
Water0
1
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)153,88612
Polymers152,5596
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54520 Å2
ΔGint-360 kcal/mol
Surface area51530 Å2
MethodPISA
2
G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
I: Fusion glycoprotein F0
L: Fusion glycoprotein F0
M: Fusion glycoprotein F0
N: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,88612
Polymers152,5596
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54740 Å2
ΔGint-368 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.170, 131.500, 164.280
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fusion glycoprotein F0


Mass: 9529.798 Da / Num. of mol.: 6 / Fragment: unp residues 26-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: paH / Cell line (production host): HEK293F / Production host: homo sapiens (human) / References: UniProt: Q84850
#2: Protein
Fusion glycoprotein F0


Mass: 41323.137 Da / Num. of mol.: 6 / Fragment: unp residues 147-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: paH / Cell line (production host): HEK293F / Production host: homo sapiens (human) / References: UniProt: Q84850, UniProt: P03420*PLUS
#3: 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.: 12
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
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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% (w/v) PEG 3000, 0.1 M sodium citrate, pH 5.5, 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 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 114379 / Num. obs: 76177 / % possible obs: 66.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1902 / % possible all: 16.7

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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 1G2C

1g2c


Resolution: 2.821→44.209 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 3586 4.99 %random
Rwork0.2213 ---
obs0.2233 71850 63.71 %-
all-112776 --
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.091 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4863 Å20 Å23.0705 Å2
2---1.9715 Å20 Å2
3---2.4578 Å2
Refinement stepCycle: LAST / Resolution: 2.821→44.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19947 0 168 0 20115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520445
X-RAY DIFFRACTIONf_angle_d0.85627638
X-RAY DIFFRACTIONf_dihedral_angle_d15.4547618
X-RAY DIFFRACTIONf_chiral_restr0.0493361
X-RAY DIFFRACTIONf_plane_restr0.0033448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8213-2.85850.32130.355276X-RAY DIFFRACTION2
2.8585-2.89760.5517110.3987219X-RAY DIFFRACTION5
2.8976-2.9390.4509160.3487407X-RAY DIFFRACTION10
2.939-2.98290.3872420.3319552X-RAY DIFFRACTION14
2.9829-3.02950.4132300.3492711X-RAY DIFFRACTION18
3.0295-3.07910.326470.3585896X-RAY DIFFRACTION22
3.0791-3.13220.3873580.33141111X-RAY DIFFRACTION27
3.1322-3.18910.3651730.32311305X-RAY DIFFRACTION32
3.1891-3.25050.3481710.30361588X-RAY DIFFRACTION38
3.2505-3.31680.32880.3011956X-RAY DIFFRACTION48
3.3168-3.38890.34291340.30382364X-RAY DIFFRACTION58
3.3889-3.46770.35761500.29282767X-RAY DIFFRACTION67
3.4677-3.55440.32351640.27553016X-RAY DIFFRACTION73
3.5544-3.65040.34591620.26033251X-RAY DIFFRACTION79
3.6504-3.75780.31831710.24943467X-RAY DIFFRACTION84
3.7578-3.8790.25571900.2283647X-RAY DIFFRACTION89
3.879-4.01760.25052210.21563860X-RAY DIFFRACTION94
4.0176-4.17830.25151810.17684044X-RAY DIFFRACTION98
4.1783-4.36830.21562310.1644093X-RAY DIFFRACTION99
4.3683-4.59840.20382300.15744079X-RAY DIFFRACTION99
4.5984-4.88610.18922260.16574107X-RAY DIFFRACTION99
4.8861-5.26280.21012000.16984137X-RAY DIFFRACTION100
5.2628-5.79140.25812060.20314121X-RAY DIFFRACTION100
5.7914-6.6270.26482290.22164133X-RAY DIFFRACTION100
6.627-8.34020.22322130.20574151X-RAY DIFFRACTION100
8.3402-44.21460.24122390.23664206X-RAY DIFFRACTION99
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)
10.3189-0.1506-0.15630.2667-0.07530.12810.08190.19620.0011-0.2099-0.1668-0.0533-0.0734-0.0616-0.07990.1952-0.00130.05320.15040.05490.0925-41.65369.4345-49.2061
20.7238-0.1373-0.43190.30840.16580.17470.2104-0.02490.3159-0.1412-0.0171-0.2099-0.12330.02390.00870.13790.0348-0.01810.20080.1595-0.039-34.57521.0118-45.3319
30.4526-0.2299-0.33240.3245-0.0460.0890.0627-0.08270.0652-0.1788-0.0642-0.1244-0.03040.0483-0.01490.0842-0.0117-0.07310.1878-0.02570.0374-34.97299.428-36.8278
40.1594-0.1315-0.23190.23830.2640.2995-0.00590.2108-0.216-0.0331-0.170.16790.0425-0.18850.1750.0963-0.07440.03560.1689-0.08540.2938-57.5284-33.4009-38.9492
50.5885-0.1411-0.62650.11560.26590.5061-0.08050.0391-0.2932-0.0101-0.1080.1398-0.0008-0.00840.11440.0751-0.0055-0.02360.13090.01980.1267-49.6797-32.7095-27.1417
60.2998-0.2436-0.24530.08610.09920.2478-0.23190.0621-0.31980.0662-0.02690.10260.1724-0.0570.20120.1549-0.10080.16020.0632-0.1090.3838-57.1201-44.4103-30.135
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
7X-RAY DIFFRACTION4CHAIN G or CHAIN H
8X-RAY DIFFRACTION4CHAIN G or CHAIN H
9X-RAY DIFFRACTION5CHAIN I or CHAIN L
10X-RAY DIFFRACTION5CHAIN I or CHAIN L
11X-RAY DIFFRACTION6CHAIN M or CHAIN N
12X-RAY DIFFRACTION6CHAIN M or CHAIN N

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