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- PDB-3rki: Structural basis for immunization with post-fusion RSV F to elici... -

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Basic information

Entry
Database: PDB / ID: 3rki
TitleStructural basis for immunization with post-fusion RSV F to elicit high neutralizing antibody titers
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Fusion Protein
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
Helix Hairpins - #2480 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSwanson, K.A. / Settembre, E.C. / Shaw, C.A. / Dey, A.K. / Rappuoli, R. / Mandl, C.W. / Dormitzer, P.D. / Carfi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for immunization with postfusion respiratory syncytial virus fusion F glycoprotein (RSV F) to elicit high neutralizing antibody titers.
Authors: Swanson, K.A. / Settembre, E.C. / Shaw, C.A. / Dey, A.K. / Rappuoli, R. / Mandl, C.W. / Dormitzer, P.R. / Carfi, A.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,23110
Polymers175,4633
Non-polymers2,7687
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36830 Å2
ΔGint-211 kcal/mol
Surface area55430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.930, 113.160, 311.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLNGLNAA27 - 9827 - 98
21ASNASNGLNGLNBB27 - 9827 - 98
31ASNASNGLNGLNCC27 - 9827 - 98
12GLYGLYLEULEUAA162 - 321153 - 312
22GLYGLYLEULEUBB162 - 321153 - 312
32GLYGLYLEULEUCC162 - 321153 - 312
13LEULEUASNASNAA334 - 517325 - 508
23LEULEUASNASNBB334 - 517325 - 508
33LEULEUASNASNCC334 - 517325 - 508

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Components

#1: Protein Fusion glycoprotein F0 / Protein F / Fusion glycoprotein F2 / Fusion glycoprotein F1


Mass: 58487.637 Da / Num. of mol.: 3 / Fragment: Respiratory Syncytial Virus F, residues 1-524
Source method: isolated from a genetically manipulated source
Details: Fusion Peptide deleted / Source: (gene. exp.) Human respiratory syncytial virus / Gene: F / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03420
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.41 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 4.2 M Sodium Formate, 100 mM Sodium Acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 52224 / Num. obs: 51911 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.3 Å

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KPE and 1ZTM

3kpe

1ztm


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.856 / SU B: 48.729 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26428 2065 5.1 %RANDOM
Rwork0.22798 ---
obs0.22984 38122 77.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.264 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å20 Å2
2---1.72 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10256 0 182 0 10438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02210614
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.98414410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.36851311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.69426.276427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.676151937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1171527
X-RAY DIFFRACTIONr_chiral_restr0.130.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217607
X-RAY DIFFRACTIONr_mcbond_it0.5181.56569
X-RAY DIFFRACTIONr_mcangle_it1.071210744
X-RAY DIFFRACTIONr_scbond_it1.93234045
X-RAY DIFFRACTIONr_scangle_it3.6914.53666
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1664TIGHT POSITIONAL0.060.05
2B1664TIGHT POSITIONAL0.060.05
3C1664TIGHT POSITIONAL0.060.05
1A1585LOOSE POSITIONAL0.075
2B1585LOOSE POSITIONAL0.075
3C1585LOOSE POSITIONAL0.075
1A1664TIGHT THERMAL0.10.5
2B1664TIGHT THERMAL0.090.5
3C1664TIGHT THERMAL0.090.5
1A1585LOOSE THERMAL0.1110
2B1585LOOSE THERMAL0.110
3C1585LOOSE THERMAL0.110
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 42 -
Rwork0.338 682 -
obs--19.24 %
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)
10.9323-0.1190.55620.1647-0.51063.4106-0.03650.1937-0.28510.0148-0.0448-0.01020.420.20530.08130.1266-0.00130.04130.1059-0.04090.225517.74669.45217.4624
20.9859-0.04490.96270.1157-0.22793.01070.19690.1774-0.5493-0.01540.0499-0.04790.86130.1429-0.24680.45250.05340.08230.1088-0.09520.520419.4468-4.50316.0363
31.1836-0.39291.01870.3063-0.7782.91880.0136-0.0439-0.5083-0.03740.06790.07730.6217-0.322-0.08150.3072-0.12090.07310.1561-0.00390.36026.64160.91519.3262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 517
2X-RAY DIFFRACTION2B26 - 517
3X-RAY DIFFRACTION3C26 - 517

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