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- PDB-3bgf: X-ray crystal structure of the SARS coronavirus spike receptor bi... -

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Basic information

Entry
Database: PDB / ID: 3bgf
TitleX-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab
Components
  • (F26G19 Fab) x 2
  • Spike protein S1
KeywordsViral Protein/Immune System / antigen-antibody complex / Envelope protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Virion / Virulence / Viral Protein-Immune System COMPLEX
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSARS coronavirus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsPak, J.E. / Rini, J.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural insights into immune recognition of the severe acute respiratory syndrome coronavirus S protein receptor binding domain.
Authors: Pak, J.E. / Sharon, C. / Satkunarajah, M. / Auperin, T.C. / Cameron, C.M. / Kelvin, D.J. / Seetharaman, J. / Cochrane, A. / Plummer, F.A. / Berry, J.D. / Rini, J.M.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 31, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / entity_src_nat / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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
S: Spike protein S1
A: Spike protein S1
L: F26G19 Fab
H: F26G19 Fab
C: F26G19 Fab
B: F26G19 Fab


Theoretical massNumber of molelcules
Total (without water)137,8906
Polymers137,8906
Non-polymers00
Water1086
1
A: Spike protein S1
C: F26G19 Fab
B: F26G19 Fab


Theoretical massNumber of molelcules
Total (without water)68,9453
Polymers68,9453
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
MethodPISA
2
S: Spike protein S1
L: F26G19 Fab
H: F26G19 Fab


Theoretical massNumber of molelcules
Total (without water)68,9453
Polymers68,9453
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.688, 73.365, 110.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21C
12H
22B
32H
42B
52H
62B
72H
82B
13S
23A
14H
24B
15L
25C
16L
26C
17S
27A
37S
47A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLUGLU2LC1 - 1051 - 105
211ASPASPGLUGLU2CE1 - 1051 - 105
112GLNGLNILEILE2HD3 - 513 - 51
212GLNGLNILEILE2BF3 - 513 - 51
322GLYGLYGLUGLU2HD53 - 8154 - 82
422GLYGLYGLUGLU2BF53 - 8154 - 82
532THRTHRGLNGLN2HD83 - 9987 - 103
632THRTHRGLNGLN2BF83 - 9987 - 103
742ASPASPTHRTHR4HD101 - 110109 - 118
842ASPASPTHRTHR4BF101 - 110109 - 118
113ASPASPSERSER2SA385 - 50068 - 183
213ASPASPSERSER2AB385 - 50068 - 183
114THRTHRHOHHOH2HD - H117 - 215125
214THRTHRHOHHOH2BF - I117 - 215125
115ASPASPGLUGLU2LC110 - 187110 - 187
215ASPASPGLUGLU2CE110 - 187110 - 187
116HISHISASNASN2LC189 - 210189 - 210
216HISHISASNASN2CE189 - 210189 - 210
117PROPROLEULEU4SA324 - 3557 - 38
217PROPROLEULEU4AB324 - 3557 - 38
327SERSERALAALA4SA358 - 38441 - 67
427SERSERALAALA4AB358 - 38441 - 67

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein Spike protein S1


Mass: 21858.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Strain: TOR2 / Gene: S, 2 / Plasmid: pPA-TEV / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P59594
#2: Antibody F26G19 Fab


Mass: 23458.869 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Antibody F26G19 Fab


Mass: 23627.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES, 14% PEG 20000, 10-15% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 18, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 37614 / Num. obs: 35508 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.132 / Χ2: 1.11 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.92.90.75125871.09269.9
2.9-3.023.70.61130631.1582.4
3.02-3.154.40.5134251.14192.5
3.15-3.325.10.40536521.14298.9
3.32-3.535.60.28837131.132100
3.53-3.85.70.19537341.146100
3.8-4.185.70.12737331.117100
4.18-4.795.80.08137781.115100
4.79-6.035.90.07538301.199.9
6.03-505.60.04439930.99699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.04 Å10 Å
Translation4.04 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2DDB, 1KEG

2ddb

1keg


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.85 / SU B: 46.401 / SU ML: 0.397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1495 4.9 %RANDOM
Rwork0.234 ---
obs0.237 30321 98.73 %-
all-30760 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.995 Å2
Baniso -1Baniso -2Baniso -3
1-7.4 Å20 Å20 Å2
2---0.5 Å20 Å2
3----6.9 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9411 0 0 6 9417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229669
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.95213174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.20451201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98523.829397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.486151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7181543
X-RAY DIFFRACTIONr_chiral_restr0.0740.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027333
X-RAY DIFFRACTIONr_nbd_refined0.2460.34096
X-RAY DIFFRACTIONr_nbtor_refined0.3280.56596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5509
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4260.55
X-RAY DIFFRACTIONr_mcbond_it0.64726142
X-RAY DIFFRACTIONr_mcangle_it1.13939802
X-RAY DIFFRACTIONr_scbond_it0.33624075
X-RAY DIFFRACTIONr_scangle_it0.54833372
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 96 -
Rwork0.307 1882 -
all-1978 -
obs--89.38 %

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