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- PDB-5c69: Crystal Structure of Prefusion-stabilized RSV F variant PR-DM -

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Basic information

Entry
Database: PDB / ID: 5c69
TitleCrystal Structure of Prefusion-stabilized RSV F variant PR-DM
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: 2.3 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
A: Fusion glycoprotein F0,Fibritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,70715
Polymers54,4431
Non-polymers1,26414
Water3,117173
1
A: Fusion glycoprotein F0,Fibritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)334,24490
Polymers326,6586
Non-polymers7,58684
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 area46130 Å2
ΔGint-949 kcal/mol
Surface area95980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.820, 167.820, 167.820
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
11A-610-

CL

21A-843-

HOH

31A-865-

HOH

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Components

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


Mass: 54443.020 Da / Num. of mol.: 1 / Fragment: F2 subunit, F1 subunit ectodomain / Mutation: N67I, S215P, 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 65.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 1.24M 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: 2.3→46.54 Å / Num. all: 36440 / Num. obs: 36440 / % possible obs: 100 % / Redundancy: 11.6 % / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12 % / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 1.8 / % 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: 4MMR

4mmr


Resolution: 2.3→46.54 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1834 5.04 %Random
Rwork0.1803 34550 --
obs0.1821 36384 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.42 Å2 / Biso mean: 56.6179 Å2 / Biso min: 26.23 Å2
Refinement stepCycle: final / Resolution: 2.3→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 66 173 3689
Biso mean--106.12 48 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053572
X-RAY DIFFRACTIONf_angle_d0.8584839
X-RAY DIFFRACTIONf_chiral_restr0.032580
X-RAY DIFFRACTIONf_plane_restr0.003599
X-RAY DIFFRACTIONf_dihedral_angle_d13.8271309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3004-2.36260.28761310.271126102741
2.3626-2.43210.27911150.248626182733
2.4321-2.51060.31161510.246325982749
2.5106-2.60040.25481400.235726012741
2.6004-2.70450.28381530.226826112764
2.7045-2.82750.25591550.220126112766
2.8275-2.97660.24391250.218826372762
2.9766-3.1630.27531320.197826492781
3.163-3.40720.24451500.184726282778
3.4072-3.74990.19011290.155826862815
3.7499-4.29220.16391550.147126822837
4.2922-5.40640.16981390.137427342873
5.4064-46.55440.20831590.175828853044
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)
16.8715.85875.49826.68265.25124.58940.1130.141-0.422-0.25320.1691-0.72350.08860.8015-0.39960.31610.09260.04190.36970.08510.463936.10540.006211.4558
28.38920.02792.77121.098-1.08742.8738-0.22351.19210.1791-0.24350.04620.01360.07570.42780.11020.3546-0.04520.05740.3518-0.07350.259912.95516.9513-14.213
31.7543-3.02080.9055.3284-1.60123.47760.562-0.2742-0.63630.7325-0.32160.5389-0.26980.2678-0.23671.1381-0.0041-0.35921.3920.05721.414-21.18896.7549-24.0065
42.063-0.296-0.530.24110.85333.1801-0.48450.78670.9137-0.7499-0.3276-1.3969-1.18310.42780.7840.8312-0.21470.0120.98210.02320.968-30.17-4.0693-22.856
58.39646.49955.24755.05734.07313.30740.1330.05270.84780.0824-0.30391.125-0.1619-0.47980.20270.466-0.0291-0.04410.4913-0.03650.608-16.19923.469-15.69
65.69483.065-3.25898.97561.60973.89570.78750.752-0.0749-1.0176-0.85742.0765-0.4663-0.4593-0.00971.18160.5395-0.2621.43740.05871.1180.845518.2729-6.9703
72.53021.7630.72522.95570.72852.2608-0.61471.00910.303-1.08060.51680.4703-0.39340.21160.08380.6137-0.0325-0.02620.59490.05820.3921-0.86668.7379-22.0988
83.02950.27721.46430.96160.25931.3426-0.02630.3813-0.1544-0.1690.0082-0.03470.14390.02030.02770.3001-0.03310.05680.2556-0.00440.249610.08112.9293-8.4546
91.05740.1871-0.06561.5431-0.87923.22740.0279-0.033-0.0510.1623-0.0283-0.3139-0.17590.3267-0.00670.24580.0125-0.00760.32050.02890.359530.78825.625815.9772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 42 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 62 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 67 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 73 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 98 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 103 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 216 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 217 through 331 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 332 through 506 )B0

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