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- PDB-4mmr: Crystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 9.5 -

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Basic information

Entry
Database: PDB / ID: 4mmr
TitleCrystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 9.5
Components
  • Fusion glycoprotein F1 fused with Fibritin trimerization domain
  • Fusion glycoprotein F2
KeywordsVIRAL PROTEIN / fusion / membrane
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / 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 / virion component / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell ...symbiont-mediated induction of syncytium formation / 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 / virion component / 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 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsStewart-Jones, G.B.E. / McLellan, J.S. / Joyce, M.G. / Sastry, M. / Yang, Y. / Graham, B.S. / Kwong, P.D.
CitationJournal: Science / Year: 2013
Title: Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus.
Authors: McLellan, J.S. / Chen, M. / Joyce, M.G. / Sastry, M. / Stewart-Jones, G.B. / Yang, Y. / Zhang, B. / Chen, L. / Srivatsan, S. / Zheng, A. / Zhou, T. / Graepel, K.W. / Kumar, A. / Moin, S. / ...Authors: McLellan, J.S. / Chen, M. / Joyce, M.G. / Sastry, M. / Stewart-Jones, G.B. / Yang, Y. / Zhang, B. / Chen, L. / Srivatsan, S. / Zheng, A. / Zhou, T. / Graepel, K.W. / Kumar, A. / Moin, S. / Boyington, J.C. / Chuang, G.Y. / Soto, C. / Baxa, U. / Bakker, A.Q. / Spits, H. / Beaumont, T. / Zheng, Z. / Xia, N. / Ko, S.Y. / Todd, J.P. / Rao, S. / Graham, B.S. / Kwong, P.D.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Jun 2, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain


Theoretical massNumber of molelcules
Total (without water)54,7922
Polymers54,7922
Non-polymers00
Water00
1
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain

A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain

A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain


Theoretical massNumber of molelcules
Total (without water)164,3776
Polymers164,3776
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area37280 Å2
ΔGint-260 kcal/mol
Surface area54670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.852, 170.852, 170.852
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 F2


Mass: 9215.410 Da / Num. of mol.: 1 / Mutation: P102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Gene: F / Plasmid: p(alpha)H / Cell line (production host): FreeStyle(tm) 293-F / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1 fused with Fibritin trimerization domain


Mass: 45577.020 Da / Num. of mol.: 1 / Mutation: S190F, V207L, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2, (gene. exp.) Enterobacteria phage T4 (virus)
Gene: F / Plasmid: p(alpha)H / Cell line (production host): FreeStyle(tm) 293-F / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: P10104
Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.4M sodium potassium tartarate, 0.1M CHES, pH 9.5, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 15925 / Num. obs: 15925 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 16.899 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.305 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26403 796 5 %RANDOM
Rwork0.21891 ---
all0.2212 15925 --
obs0.2212 15085 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 123.428 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 0 0 3523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023581
X-RAY DIFFRACTIONr_bond_other_d0.0010.023485
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9684857
X-RAY DIFFRACTIONr_angle_other_deg0.8253.0038030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4295453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88326.154143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.79715661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.573159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.86312.0651818
X-RAY DIFFRACTIONr_mcbond_other8.85412.0641817
X-RAY DIFFRACTIONr_mcangle_it13.26818.0932269
X-RAY DIFFRACTIONr_mcangle_other13.26818.0962270
X-RAY DIFFRACTIONr_scbond_it9.45712.6171763
X-RAY DIFFRACTIONr_scbond_other9.45512.621764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.09718.6062589
X-RAY DIFFRACTIONr_long_range_B_refined19.06696.8224101
X-RAY DIFFRACTIONr_long_range_B_other19.06596.8434102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.101→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 53 -
Rwork0.327 985 -
obs--89.71 %

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