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- PDB-4mms: Crystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 4mms
TitleCrystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 5.5
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: 2.397 Å
AuthorsMclellan, J.S. / Joyce, M.G. / Stewart-Jones, G.B.E. / 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: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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 / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
C: Fusion glycoprotein F2
D: Fusion glycoprotein F1 fused with Fibritin trimerization domain
E: Fusion glycoprotein F2
F: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,72220
Polymers164,3776
Non-polymers1,34514
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42410 Å2
ΔGint-429 kcal/mol
Surface area50040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.753, 170.753, 163.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fusion glycoprotein F2


Mass: 9215.410 Da / Num. of mol.: 3 / 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.: 3 / 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O
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: 3.63 Å3/Da / Density % sol: 66.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.7 M ammonium sulfate, 0.1 M citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 13, 2013
RadiationMonochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. all: 95046 / Num. obs: 90864 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JHW

4jhw


Resolution: 2.397→37.859 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 4591 5.06 %Random
Rwork0.1873 ---
all0.1886 95007 --
obs0.1886 90779 95.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.397→37.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10421 0 70 522 11013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310651
X-RAY DIFFRACTIONf_angle_d0.83614418
X-RAY DIFFRACTIONf_dihedral_angle_d11.6163899
X-RAY DIFFRACTIONf_chiral_restr0.0561734
X-RAY DIFFRACTIONf_plane_restr0.0031804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3973-2.42450.29871560.26472805X-RAY DIFFRACTION95
2.4245-2.4530.31851320.26132935X-RAY DIFFRACTION98
2.453-2.4830.26771770.25172861X-RAY DIFFRACTION97
2.483-2.51440.30941440.24492916X-RAY DIFFRACTION97
2.5144-2.54750.30091480.24872869X-RAY DIFFRACTION97
2.5475-2.58240.29921650.25022892X-RAY DIFFRACTION98
2.5824-2.61920.27091550.24082881X-RAY DIFFRACTION97
2.6192-2.65830.29011610.23772897X-RAY DIFFRACTION97
2.6583-2.69980.27071660.24152876X-RAY DIFFRACTION97
2.6998-2.74410.27271470.23582906X-RAY DIFFRACTION97
2.7441-2.79140.2981460.2352882X-RAY DIFFRACTION97
2.7914-2.84210.27021400.23522905X-RAY DIFFRACTION97
2.8421-2.89680.28151470.22722887X-RAY DIFFRACTION97
2.8968-2.95590.24131570.23222878X-RAY DIFFRACTION97
2.9559-3.02010.26241360.22112898X-RAY DIFFRACTION97
3.0201-3.09040.23681520.22112870X-RAY DIFFRACTION96
3.0904-3.16760.24911620.21142874X-RAY DIFFRACTION96
3.1676-3.25320.23941530.21052864X-RAY DIFFRACTION96
3.2532-3.34890.23721560.20332887X-RAY DIFFRACTION95
3.3489-3.45690.22951580.18462841X-RAY DIFFRACTION96
3.4569-3.58040.20951590.17392882X-RAY DIFFRACTION96
3.5804-3.72360.1871660.16952846X-RAY DIFFRACTION95
3.7236-3.89290.22011530.17062879X-RAY DIFFRACTION95
3.8929-4.09790.16331440.16492845X-RAY DIFFRACTION95
4.0979-4.35430.16481500.14382844X-RAY DIFFRACTION94
4.3543-4.690.15821480.13442860X-RAY DIFFRACTION94
4.69-5.16090.17011770.14192817X-RAY DIFFRACTION93
5.1609-5.90520.18661480.17522861X-RAY DIFFRACTION93
5.9052-7.43080.2011450.19032859X-RAY DIFFRACTION91
7.4308-37.86390.19121430.17882871X-RAY DIFFRACTION88

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