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- PDB-5k6g: Crystal structure of prefusion-stabilized RSV F single-chain 9-24... -

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Basic information

Entry
Database: PDB / ID: 5k6g
TitleCrystal structure of prefusion-stabilized RSV F single-chain 9-24 DS-Cav1 variant.
ComponentsFusion glycoprotein F0,Fusion glycoprotein F0
KeywordsVIRAL PROTEIN / Respiratory Syncytial Virus / Prefusion / Vaccine / Stabilized
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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 / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJoyce, M.G. / Zhang, B. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV.
Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / ...Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / Pancera, M. / Sastry, M. / Soto, C. / Stewart-Jones, G.B. / Thomas, P.V. / Van Galen, J.G. / Baxa, U. / Lee, K.K. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Fusion glycoprotein F0,Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)49,1731
Polymers49,1731
Non-polymers00
Water00
1
F: Fusion glycoprotein F0,Fusion glycoprotein F0

F: Fusion glycoprotein F0,Fusion glycoprotein F0

F: Fusion glycoprotein F0,Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)147,5193
Polymers147,5193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11660 Å2
ΔGint-31 kcal/mol
Surface area54730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.147, 168.147, 168.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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


Mass: 49173.000 Da / Num. of mol.: 1
Fragment: UNP residues 26-79 and UNP residues 145-509 linked via LINKER residues GS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A / Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420

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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: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaOAc-Acetic Acid pH 5.5, 1.82 M Li2SO4, 0.1 M MgSO4, 5 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46.64 Å / Num. obs: 18674 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.8
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K6B

5k6b


Resolution: 2.9→46.636 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 902 4.86 %RANDOM
Rwork0.2301 ---
obs0.2328 18561 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 0 3438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023504
X-RAY DIFFRACTIONf_angle_d0.4734754
X-RAY DIFFRACTIONf_dihedral_angle_d13.7472173
X-RAY DIFFRACTIONf_chiral_restr0.041571
X-RAY DIFFRACTIONf_plane_restr0.002598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9004-3.08210.37721370.32372867X-RAY DIFFRACTION100
3.0821-3.320.35631460.29522862X-RAY DIFFRACTION100
3.32-3.6540.32031580.23822902X-RAY DIFFRACTION100
3.654-4.18240.28421640.22542902X-RAY DIFFRACTION100
4.1824-5.26820.23641430.18962976X-RAY DIFFRACTION100
5.2682-46.64160.28561540.2343150X-RAY DIFFRACTION100
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)
11.253-0.5075-1.11213.10631.30761.20630.15930.1674-0.16230.07090.1703-0.26580.4577-0.1719-0.06650.7260.0223-0.1440.66840.05910.53692.8679-6.934213.684
22.45280.9360.89293.8034-0.76643.0706-0.12920.66550.341-0.59920.0091-0.0906-0.25830.69120.07570.9714-0.04010.05341.184-0.24820.92453.9434-15.3613-14.0438
34.1482-0.3372.75742.6863-0.02267.38890.36930.4688-0.8687-0.17830.1347-0.16521.52710.8571-0.57781.13510.1199-0.12120.6561-0.16081.01077.1095-24.9645-1.352
41.59270.71310.64661.71061.99372.90.03030.0945-0.08430.11940.03280.39850.3338-0.0766-0.09540.76560.0318-0.05070.60060.0610.78743.5734-5.558414.6271
53.39342.1145-0.37475.54740.81642.5799-0.25870.1580.1835-0.32770.30690.12390.28980.00910.18970.8980.0991-0.040.77350.04040.75548.32352.05327.5367
64.39720.18731.19512.5381-0.2983.0550.1739-0.23390.25870.2808-0.1002-0.1617-0.09960.2193-0.07420.90470.10490.04610.6958-0.08610.79965.629222.950132.7241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 73 )
2X-RAY DIFFRACTION2chain 'F' and (resid 74 through 100 )
3X-RAY DIFFRACTION3chain 'F' and (resid 101 through 216 )
4X-RAY DIFFRACTION4chain 'F' and (resid 217 through 352 )
5X-RAY DIFFRACTION5chain 'F' and (resid 353 through 383 )
6X-RAY DIFFRACTION6chain 'F' and (resid 384 through 509 )

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