[English] 日本語
Yorodumi
- PDB-8fi9: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fi9
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001
Components
  • (WRAIR-5001 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / SARS-CoV-2 / coronavirus / immune system / antibody / nonhuman primate / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsSankhala, R.S. / Jensen, J.L. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Nat Commun / Year: 2024
Title: Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.
Authors: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. ...Authors: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. / Chen, W.H. / Donofrio, G.C. / Jian, N. / King, H.A.D. / Lorang, C.G. / Martinez, E.J. / Rees, P.A. / Peterson, C.E. / Schmidt, F. / Hart, T.J. / Duso, D.K. / Kummer, L.W. / Casey, S.P. / Williams, J.K. / Kannan, S. / Slike, B.M. / Smith, L. / Swafford, I. / Thomas, P.V. / Tran, U. / Currier, J.R. / Bolton, D.L. / Davidson, E. / Doranz, B.J. / Hatziioannou, T. / Bieniasz, P.D. / Paquin-Proulx, D. / Reiley, W.W. / Rolland, M. / Sullivan, N.J. / Vasan, S. / Collins, N.D. / Modjarrad, K. / Gromowski, G.D. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
History
DepositionDec 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
C: Spike protein S1
F: WRAIR-5001 Fab Light chain
G: WRAIR-5001 Fab Heavy chain
H: WRAIR-5001 Fab Heavy chain
I: WRAIR-5001 Fab Light chain
J: WRAIR-5001 Fab Heavy chain
K: Spike protein S1
L: WRAIR-5001 Fab Light chain
N: WRAIR-5001 Fab Light chain
O: Spike protein S1
Q: WRAIR-5001 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,46226
Polymers280,65612
Non-polymers1,80614
Water724
1
A: Spike protein S1
H: WRAIR-5001 Fab Heavy chain
L: WRAIR-5001 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5696
Polymers70,1643
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spike protein S1
F: WRAIR-5001 Fab Light chain
G: WRAIR-5001 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3854
Polymers70,1643
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: WRAIR-5001 Fab Light chain
J: WRAIR-5001 Fab Heavy chain
O: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5696
Polymers70,1643
Non-polymers4053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: Spike protein S1
N: WRAIR-5001 Fab Light chain
Q: WRAIR-5001 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93810
Polymers70,1643
Non-polymers7747
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.508, 115.565, 142.167
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 2 types, 8 molecules FILNGHJQ

#2: Antibody
WRAIR-5001 Fab Light chain


Mass: 22972.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody
WRAIR-5001 Fab Heavy chain


Mass: 24118.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 8 molecules ACKO

#1: Protein
Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 4 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: isolated from a natural 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

-
Non-polymers , 2 types, 14 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M Phosphate-citrate pH 4.5, 20% w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.19→87.31 Å / Num. obs: 31815 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.981 / Net I/σ(I): 1.1
Reflection shellResolution: 4.19→4.42 Å / Num. unique obs: 4553 / CC1/2: 0.348

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→19.99 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 1550 5 %
Rwork0.2521 --
obs0.2543 30971 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17835 0 116 4 17955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318398
X-RAY DIFFRACTIONf_angle_d0.6125061
X-RAY DIFFRACTIONf_dihedral_angle_d6.8242583
X-RAY DIFFRACTIONf_chiral_restr0.0462754
X-RAY DIFFRACTIONf_plane_restr0.0043237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.330.38371460.36362628X-RAY DIFFRACTION100
4.33-4.490.38931330.3382656X-RAY DIFFRACTION100
4.49-4.660.32081390.29862692X-RAY DIFFRACTION100
4.66-4.870.3681450.29272639X-RAY DIFFRACTION100
4.87-5.130.31111380.292667X-RAY DIFFRACTION100
5.13-5.440.33251410.27542687X-RAY DIFFRACTION100
5.44-5.850.311390.26732645X-RAY DIFFRACTION100
5.85-6.420.32921410.27222692X-RAY DIFFRACTION100
6.42-7.310.27951400.26132685X-RAY DIFFRACTION100
7.31-9.070.29881410.22722689X-RAY DIFFRACTION100
9.07-19.990.22541470.19182741X-RAY DIFFRACTION100
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)
14.7805-1.4244.74243.108-2.97636.8008-0.6044-0.07130.22230.04920.09970.4017-0.0051-1.09740.60722.1576-0.11570.08582.1245-0.1871.9528.708615.54266.4311
27.0184-3.78813.36335.3883-1.59844.2655-0.44810.54740.03210.188-0.11510.2863-0.37460.1280.4951.9994-0.16630.09441.93970.0591.845722.397424.569259.5192
38.0706-2.6512-0.94656.03860.75739.1550.1394-0.2216-0.9124-0.5117-0.5124-0.02770.00310.46220.312.11790.0052-0.02282.0450.06371.953169.4436-13.691653.7341
43.4043-2.27974.01527.3073-7.24957.5579-0.77290.14980.87940.1874-0.6525-0.7065-0.89460.99381.4523.25220.2752-0.25563.21430.07472.237466.968217.80824.3216
57.4638-1.6813-0.71026.97921.75737.3484-0.1375-0.4426-0.0641-0.5418-0.08370.02610.25280.33850.24271.59480.0501-0.0771.05570.12971.63347.90150.481583.4198
63.4168-1.1852.08724.1548-3.73634.8008-0.4346-0.4044-0.01680.30050.62160.4499-0.5374-0.44410.06782.96670.30560.10132.9351-0.08271.841349.812613.674624.0643
75.15581.7897-2.51844.7247-0.26465.67830.3635-0.03150.40450.67-1.15641.09380.7382-0.70060.68181.8729-0.264-0.02822.2403-0.35182.3552138.18511.969694.9415
85.84742.49911.54514.36190.20934.8237-0.68410.0065-1.30550.7752-0.55280.60541.0447-1.74341.07892.6737-0.52480.7382.7826-0.8063.3182119.2911-6.8647101.6147
97.1617-5.4544-1.61864.6764-0.28965.5932-0.0315-0.18180.59020.5044-0.12820.0701-0.8849-0.18760.13322.8429-0.2659-0.19912.6196-0.31272.339396.610927.795126.2279
103.73713.99221.364.44843.07222.94640.3792-1.33691.00820.4666-0.5060.9815-0.00080.12610.01772.39810.0574-0.07653.0826-0.11732.248770.1048-5.6683116.1538
117.7454-2.43270.28063.64091.24775.2268-0.6729-1.1409-0.87910.17270.20530.38510.29270.48590.45162.3567-0.19950.14382.17960.20461.8975132.580210.8605121.2257
123.10783.14652.73396.29584.1563.4511-0.4971-0.42480.5245-0.25870.46-0.0471-0.2850.06180.02212.39540.0574-0.28182.416-0.0822.054377.4461-3.452599.9882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'L' and resid 1 through 212)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 215)
3X-RAY DIFFRACTION3(chain 'C' and resid 333 through 530)
4X-RAY DIFFRACTION4(chain 'F' and resid 1 through 208)
5X-RAY DIFFRACTION5(chain 'A' and resid 333 through 530)
6X-RAY DIFFRACTION6(chain 'G' and resid 2 through 215)
7X-RAY DIFFRACTION7(chain 'I' and resid 2 through 108)
8X-RAY DIFFRACTION8(chain 'J' and resid 3 through 111)
9X-RAY DIFFRACTION9(chain 'K' and resid 334 through 527)
10X-RAY DIFFRACTION10(chain 'N' and resid 1 through 210)
11X-RAY DIFFRACTION11(chain 'O' and resid 332 through 527)
12X-RAY DIFFRACTION12(chain 'Q' and resid 2 through 216)

+
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