[English] 日本語
Yorodumi
- PDB-2ghw: Crystal structure of SARS spike protein receptor binding domain i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ghw
TitleCrystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R
Components
  • Spike glycoprotein
  • anti-sars scFv antibody, 80R
KeywordsVIRUS/VIRAL PROTEIN/ANTIBIOTIC / SARS / S protein / neutralizing antibody / VIRUS-VIRAL PROTEIN-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / immunoglobulin complex / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / adaptive immune response / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / immunoglobulin complex / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / adaptive immune response / 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 / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily ...Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Alpha-Beta Plaits / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Single-chain Fv
Similarity search - Component
Biological speciesSARS coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHwang, W.C. / Lin, Y. / Santelli, E. / Sui, J. / Jaroszewski, L. / Stec, B. / Farzan, M. / Marasco, W.A. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R.
Authors: Hwang, W.C. / Lin, Y. / Santelli, E. / Sui, J. / Jaroszewski, L. / Stec, B. / Farzan, M. / Marasco, W.A. / Liddington, R.C.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE SEQUENCE OF ANTI-SARS SCFV ANTIBODY, 80R IS NOT AVAILABLE AT UNIPROT SEQUENCE DATABASE ...SEQUENCE THE SEQUENCE OF ANTI-SARS SCFV ANTIBODY, 80R IS NOT AVAILABLE AT UNIPROT SEQUENCE DATABASE AT THE TIME OF PROCESSING.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike glycoprotein
B: anti-sars scFv antibody, 80R
C: Spike glycoprotein
D: anti-sars scFv antibody, 80R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8549
Polymers98,6764
Non-polymers1775
Water8,467470
1
A: Spike glycoprotein
B: anti-sars scFv antibody, 80R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4806
Polymers49,3382
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-41 kcal/mol
Surface area18620 Å2
MethodPISA
2
C: Spike glycoprotein
D: anti-sars scFv antibody, 80R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3743
Polymers49,3382
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-20 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.453, 175.902, 67.561
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
51A
61C
12B
22D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUVALVALAA322 - 3499 - 36
211LEULEUVALVALCC322 - 3499 - 36
321PHEPHEVALVALAA361 - 36948 - 56
421PHEPHEVALVALCC361 - 36948 - 56
531ASNASNGLUGLUAA381 - 50268 - 189
631ASNASNGLUGLUCC381 - 50268 - 189
112GLUGLUSERSERBB1 - 2403 - 242
212GLUGLUSERSERDD1 - 2403 - 242

NCS ensembles :
ID
1
2

-
Components

#1: Protein Spike glycoprotein / Peplomer protein / E2 / RBD


Mass: 22883.830 Da / Num. of mol.: 2 / Fragment: RBD of spike protein S1 (318-510)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: S / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594
#2: Antibody anti-sars scFv antibody, 80R


Mass: 26454.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q65ZC9
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 51915 / Num. obs: 51915 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.1 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.8
Reflection shellResolution: 2.29→2.38 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.9 / % possible all: 87

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJF CHAIN F, 1DZB CHAIN A

2ajf

1dzb


Resolution: 2.3→45.55 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.848 / SU B: 37.1 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29537 2308 5.1 %RANDOM
Rwork0.24843 ---
obs0.25085 43380 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20.51 Å2
2---2.58 Å20 Å2
3---4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 5 470 7089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226802
X-RAY DIFFRACTIONr_bond_other_d0.0010.024620
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9479266
X-RAY DIFFRACTIONr_angle_other_deg0.853.00311135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32323.141312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2681547
X-RAY DIFFRACTIONr_chiral_restr0.0730.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021503
X-RAY DIFFRACTIONr_nbd_refined0.1650.21192
X-RAY DIFFRACTIONr_nbd_other0.190.24902
X-RAY DIFFRACTIONr_nbtor_refined0.180.23162
X-RAY DIFFRACTIONr_nbtor_other0.0790.23726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5241.55330
X-RAY DIFFRACTIONr_mcbond_other0.0691.51699
X-RAY DIFFRACTIONr_mcangle_it0.61226760
X-RAY DIFFRACTIONr_scbond_it0.87733225
X-RAY DIFFRACTIONr_scangle_it1.3084.52506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A930tight positional0.030.05
2B1319tight positional0.030.05
1A1487medium positional0.140.5
2B1983medium positional0.130.5
1A930tight thermal0.090.5
2B1319tight thermal0.080.5
1A1487medium thermal0.752
2B1983medium thermal0.712
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 169 -
Rwork0.301 2990 -
obs--87.39 %
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)
12.2784-0.68140.75472.19580.31511.3683-0.0176-0.0623-0.15420.09590.0020.04260.1855-0.00730.0156-0.1336-0.03910.066-0.1788-0.0009-0.1579-3.327-24.40415.357
22.1035-0.5523-0.82722.1672-0.28711.15550.0445-0.04940.16470.0373-0.0597-0.1275-0.17380.03460.0152-0.1368-0.032-0.0491-0.1580.0149-0.146627.22356.96315.233
33.03560.5675-0.20132.6452-0.27610.51130.0736-0.12910.2510.1468-0.0906-0.2222-0.03610.12620.0171-0.16240.00070.0469-0.1586-0.0311-0.184413.6841.8623.45
42.240.85260.20432.79060.02230.70730.0977-0.2278-0.23310.1663-0.080.2730.0181-0.1195-0.0177-0.17940.0093-0.0266-0.14410.0388-0.136410.18930.66523.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB1 - 2443 - 246
2X-RAY DIFFRACTION2CC318 - 5055 - 192
3X-RAY DIFFRACTION3DD1 - 2453 - 247
4X-RAY DIFFRACTION4AA319 - 5096 - 196

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more