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- PDB-5c6b: Crystal Structure of Prefusion-stabilized RSV F variant SC-TM -

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Basic information

Entry
Database: PDB / ID: 5c6b
TitleCrystal Structure of Prefusion-stabilized RSV F variant SC-TM
ComponentsFusion glycoprotein F0,Fibritin
KeywordsVIRAL PROTEIN / class I viral fusion protein / fusion / respiratory syncytial virus / prefusion
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
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Enterobacteria phage Ox2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMcLellan, J.S. / Langedijk, J.P.M.
CitationJournal: Nat Commun / Year: 2015
Title: A highly stable prefusion RSV F vaccine derived from structural analysis of the fusion mechanism.
Authors: Krarup, A. / Truan, D. / Furmanova-Hollenstein, P. / Bogaert, L. / Bouchier, P. / Bisschop, I.J. / Widjojoatmodjo, M.N. / Zahn, R. / Schuitemaker, H. / McLellan, J.S. / Langedijk, J.P.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
F: Fusion glycoprotein F0,Fibritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3758
Polymers54,7121
Non-polymers6627
Water2,900161
1
F: Fusion glycoprotein F0,Fibritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)332,24848
Polymers328,2746
Non-polymers3,97542
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area38350 Å2
ΔGint-521 kcal/mol
Surface area98670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.200, 168.200, 168.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-603-

SO4

21F-603-

SO4

31F-607-

CL

41F-701-

HOH

51F-815-

HOH

61F-851-

HOH

71F-859-

HOH

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Components

#1: Protein Fusion glycoprotein F0,Fibritin / Protein F


Mass: 54712.277 Da / Num. of mol.: 1 / Fragment: ectodomain
Mutation: N67I, S215P, E487Q, I379V, M447V,N67I, S215P, E487Q, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A, (gene. exp.) Enterobacteria phage Ox2 (virus)
Strain: A2 / Gene: wac / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: P03420, UniProt: Q38650
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 3.62 Å3/Da / Density % sol: 66.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 1.34M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792368 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792368 Å / Relative weight: 1
ReflectionResolution: 2.4→44.95 Å / Num. all: 32205 / Num. obs: 32205 / % possible obs: 99.7 % / Redundancy: 10.5 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.327 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMS

4mms


Resolution: 2.4→44.95 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1611 5 %Random
Rwork0.178 30582 --
obs0.1797 32193 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.28 Å2 / Biso mean: 56.316 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.4→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 35 161 3713
Biso mean--102.68 46.91 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033603
X-RAY DIFFRACTIONf_angle_d0.74874
X-RAY DIFFRACTIONf_chiral_restr0.027586
X-RAY DIFFRACTIONf_plane_restr0.003608
X-RAY DIFFRACTIONf_dihedral_angle_d13.5871330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4004-2.4710.34031390.28825082647100
2.471-2.55080.3471420.265324872629100
2.5508-2.64190.29651230.242325162639100
2.6419-2.74770.27021250.224225252650100
2.7477-2.87270.26881160.217525332649100
2.8727-3.02420.24551310.220425162647100
3.0242-3.21360.27281330.197225462679100
3.2136-3.46160.20361440.185425222666100
3.4616-3.80980.19521530.15812511266499
3.8098-4.36070.16991260.14342586271299
4.3607-5.49250.15511290.12952612274199
5.4925-44.96120.18291500.16742720287098
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)
10.41530.5474-0.31631.0192-0.01420.8867-0.09480.30830.1279-0.27390.07340.19340.1664-0.08850.03170.2562-0.06310.01230.2818-0.00840.270311.96663.222-7.7353
24.82581.76422.14231.96870.78951.0767-0.52560.65530.4999-0.60850.24380.3-0.26640.17980.20410.4474-0.04820.02450.44510.03390.3156-0.515111.6556-15.4074
36.90585.42152.45047.51922.27014.3446-0.66051.39090.7609-1.12050.8120.9843-0.0148-0.1515-0.2350.7224-0.0673-0.17510.76310.06650.5144-12.727-1.0586-27.6726
42.80380.45571.80420.78640.41721.36340.0130.3134-0.1054-0.1180.0096-0.03050.20720.0171-0.0390.2959-0.05070.03830.29660.00030.251613.21734.089-6.0539
50.82690.2525-0.10341.711-1.05683.662-0.02230.0162-0.10730.01720.0211-0.20990.14940.0487-0.00460.24080.02530.00790.27540.0160.349729.29873.002314.1526
62.61341.68370.3066.35510.66022.21890.0984-0.15750.08450.2747-0.0599-0.4667-0.09980.2878-0.08860.20850.0438-0.03710.35010.04530.185533.53239.325822.4686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 73 )F0
2X-RAY DIFFRACTION2chain 'F' and (resid 74 through 185 )F0
3X-RAY DIFFRACTION3chain 'F' and (resid 186 through 216 )F0
4X-RAY DIFFRACTION4chain 'F' and (resid 217 through 352 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 353 through 443 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 444 through 510 )F0

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