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- PDB-6ous: Structure of fusion glycoprotein from human respiratory syncytial... -

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Basic information

Entry
Database: PDB / ID: 6ous
TitleStructure of fusion glycoprotein from human respiratory syncytial virus
Components
  • (Fusion glycoprotein ...) x 2
  • RB1 Fab Heavy Chain
  • RB1 Fab Light chain
KeywordsVIRAL PROTEIN/Immune system / Antibody / RSV / Neutralizing / VIRAL PROTEIN / VIRAL PROTEIN-Immune system complex
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 / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...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 / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsSu, H.P.
CitationJournal: Nat Commun / Year: 2019
Title: A potent broadly neutralizing human RSV antibody targets conserved site IV of the fusion glycoprotein.
Authors: Tang, A. / Chen, Z. / Cox, K.S. / Su, H.P. / Callahan, C. / Fridman, A. / Zhang, L. / Patel, S.B. / Cejas, P.J. / Swoyer, R. / Touch, S. / Citron, M.P. / Govindarajan, D. / Luo, B. / Eddins, ...Authors: Tang, A. / Chen, Z. / Cox, K.S. / Su, H.P. / Callahan, C. / Fridman, A. / Zhang, L. / Patel, S.B. / Cejas, P.J. / Swoyer, R. / Touch, S. / Citron, M.P. / Govindarajan, D. / Luo, B. / Eddins, M. / Reid, J.C. / Soisson, S.M. / Galli, J. / Wang, D. / Wen, Z. / Heidecker, G.J. / Casimiro, D.R. / DiStefano, D.J. / Vora, K.A.
History
DepositionMay 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Database references / Polymer sequence / Category: entity_poly / struct_ref_seq_dif / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
G: Fusion glycoprotein F2
H: Fusion glycoprotein F1 fused with Fibritin trimerization domain
I: Fusion glycoprotein F2
J: Fusion glycoprotein F1 fused with Fibritin trimerization domain
K: Fusion glycoprotein F2
L: Fusion glycoprotein F1 fused with Fibritin trimerization domain
M: RB1 Fab Heavy Chain
N: RB1 Fab Light chain
O: RB1 Fab Heavy Chain
P: RB1 Fab Light chain
Q: RB1 Fab Heavy Chain
R: RB1 Fab Light chain
S: RB1 Fab Heavy Chain
T: RB1 Fab Light chain
U: RB1 Fab Heavy Chain
V: RB1 Fab Light chain
W: RB1 Fab Heavy Chain
X: RB1 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)623,85334
Polymers618,47624
Non-polymers5,37710
Water00
1
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
M: RB1 Fab Heavy Chain
N: RB1 Fab Light chain
O: RB1 Fab Heavy Chain
P: RB1 Fab Light chain
Q: RB1 Fab Heavy Chain
R: RB1 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,92717
Polymers309,23812
Non-polymers2,6885
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Fusion glycoprotein F2
H: Fusion glycoprotein F1 fused with Fibritin trimerization domain
I: Fusion glycoprotein F2
J: Fusion glycoprotein F1 fused with Fibritin trimerization domain
K: Fusion glycoprotein F2
L: Fusion glycoprotein F1 fused with Fibritin trimerization domain
S: RB1 Fab Heavy Chain
T: RB1 Fab Light chain
U: RB1 Fab Heavy Chain
V: RB1 Fab Light chain
W: RB1 Fab Heavy Chain
X: RB1 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,92717
Polymers309,23812
Non-polymers2,6885
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.153, 126.595, 148.165
Angle α, β, γ (deg.)87.240, 79.150, 86.290
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Fusion glycoprotein ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Fusion glycoprotein F2 / Protein F


Mass: 9512.768 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Protein
Fusion glycoprotein F1 fused with Fibritin trimerization domain / Protein F


Mass: 45609.148 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2, (gene. exp.) Human immunodeficiency virus 1
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4

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Antibody , 2 types, 12 molecules MOQSUWNPRTVX

#3: Antibody
RB1 Fab Heavy Chain


Mass: 24551.439 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody
RB1 Fab Light chain


Mass: 23406.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 10 molecules

#5: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 4
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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Details

Has ligand of interestN
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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris 8.5, 10% PEG 8000, 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.4→49.86 Å / Num. obs: 114498 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 78.54 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.127 / Rrim(I) all: 0.179 / Net I/σ(I): 3.9 / Num. measured all: 228565
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-4.160.344104047520950.7960.3440.4862.298.8
5.89-49.860.04444035220780.9940.0440.0626.699.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.96 Å
Translation3.5 Å29.96 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mmt, 1hzh

4mmt

1hzh


Resolution: 3.4→49.86 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2746 --
Rwork0.2453 --
obs-114485 98.9 %
Refinement stepCycle: LAST / Resolution: 3.4→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41241 0 356 0 41597

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