[English] 日本語
Yorodumi
- PDB-7ul0: Crystal structure of SARS-CoV-2 RBD in complex with the ridge-bin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ul0
TitleCrystal structure of SARS-CoV-2 RBD in complex with the ridge-binding nAb EH8 isolated from a nonvaccinated pediatric patient
Components
  • Heavy chain of EH8
  • Light chain of EH8
  • Spike protein S1
KeywordsVIRAL PROTEIN/Immune System / Pediatric neutralizing mAb / RBD-ridge-targeting / bind to both closed and open SARS-CoV-2 spike / Class-2 RBD-binding antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / 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 / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChen, Y. / Tolbert, W.D. / Bai, X. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentStart-up funds from the Uniformed Services University of the Health Sciences United States
CitationJournal: Iscience / Year: 2023
Title: Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD.
Authors: Chen, Y. / Prevost, J. / Ullah, I. / Romero, H. / Lisi, V. / Tolbert, W.D. / Grover, J.R. / Ding, S. / Gong, S.Y. / Beaudoin-Bussieres, G. / Gasser, R. / Benlarbi, M. / Vezina, D. / Anand, S. ...Authors: Chen, Y. / Prevost, J. / Ullah, I. / Romero, H. / Lisi, V. / Tolbert, W.D. / Grover, J.R. / Ding, S. / Gong, S.Y. / Beaudoin-Bussieres, G. / Gasser, R. / Benlarbi, M. / Vezina, D. / Anand, S.P. / Chatterjee, D. / Goyette, G. / Grunst, M.W. / Yang, Z. / Bo, Y. / Zhou, F. / Beland, K. / Bai, X. / Zeher, A.R. / Huang, R.K. / Nguyen, D.N. / Sherburn, R. / Wu, D. / Piszczek, G. / Pare, B. / Matthies, D. / Xia, D. / Richard, J. / Kumar, P. / Mothes, W. / Cote, M. / Uchil, P.D. / Lavallee, V.P. / Smith, M.A. / Pazgier, M. / Haddad, E. / Finzi, A.
History
DepositionApr 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
H: Heavy chain of EH8
L: Light chain of EH8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2636
Polymers71,5953
Non-polymers6693
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.771, 100.709, 106.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Spike protein S1


Mass: 24658.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

-
Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of EH8


Mass: 23636.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Light chain of EH8


Mass: 23299.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 2 types, 2 molecules

#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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: obtained synthetically / 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, 103 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium chloride, 0.1 M Na HEPES pH 7.5, 12% w/v PEG 8000
PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 31070 / % possible obs: 99.9 % / Redundancy: 18.8 % / Biso Wilson estimate: 57.01 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.034 / Rrim(I) all: 0.148 / Χ2: 1.193 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.49-2.5916.61.03730140.8770.2591.070.432100
2.59-2.6916.90.80530270.940.1970.8290.48499.9
2.69-2.8220.20.63830210.9660.1460.6550.521100
2.82-2.9620.30.44230330.9840.1010.4540.606100
2.96-3.1519.90.31130390.9880.0720.320.787100
3.15-3.3919.50.21930490.9930.0510.2251.062100
3.39-3.7318.40.16530540.9950.040.171.426100
3.73-4.2718.50.12130810.9960.0280.1251.9799.8
4.27-5.3819.80.10131170.9980.0230.1042.38899.9
5.38-5017.90.08432540.9980.020.0862.09399.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S4S, 7NAB

7s4s

7nab


Resolution: 2.49→46.91 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 2008 6.46 %
Rwork0.2246 29062 -
obs0.2266 31070 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.62 Å2 / Biso mean: 62.5875 Å2 / Biso min: 26.96 Å2
Refinement stepCycle: final / Resolution: 2.49→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 43 102 4971
Biso mean--96.86 49.96 -
Num. residues----632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.550.42031290.42531803193288
2.55-2.620.42191400.369820682208100
2.62-2.70.40491350.323320552190100
2.7-2.790.341420.293520842226100
2.79-2.880.34451460.272320642210100
2.88-30.32391470.275620512198100
3-3.140.32711400.286320802220100
3.14-3.30.35591440.290320822226100
3.3-3.510.29351490.231220782227100
3.51-3.780.23691440.220620852229100
3.78-4.160.22941380.201721042242100
4.16-4.760.16921540.165421222276100
4.76-60.21851440.181521412285100
6-46.910.21331560.193622452401100
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)
11.3233-0.4694-0.19340.43260.34010.96290.13940.4159-0.1545-0.38470.1252-0.01880.5440.02050.12150.61710.0847-0.04490.4544-0.15280.420922.5751-49.2248-10.6996
20.86770.0721-0.9471.18740.391.9746-0.1354-0.6758-0.74340.13460.2038-0.11341.13710.4310.25480.77940.06-0.04120.53070.27240.783723.1797-56.00532.8684
31.7014-0.10290.9492.6047-1.631.2293-0.08550.00580.1028-0.15050.1373-0.07550.02950.27180.00090.3280.00810.03890.3985-0.03560.302725.76-37.3145-5.0104
40.16620.3045-0.47260.8298-0.90540.4269-0.0270.81520.5121-0.30630.0519-0.1149-0.11830.26410.00440.5076-0.05260.01580.50350.10840.569923.6726-18.0578-14.7233
51.3309-1.48340.56741.99850.19271.37890.4127-0.66090.23730.1902-0.39670.4858-0.07810.28590.00050.33520.07060.05750.5274-0.01020.429326.0794-45.8964-3.9748
60.26012.6043-0.61613.8642-0.45341.14760.062-0.0753-0.15970.7079-0.2534-0.6698-0.09510.102-0.00050.5056-0.0097-0.08770.4610.10910.729534.9054.1575-13.3434
70.2345-0.1991-0.38980.47080.29650.47530.1370.15430.3411-0.0729-0.38571.1118-0.3367-0.38650.00350.78140.1799-0.12990.5794-0.00890.483634.771442.4093-30.169
80.97661.24090.5632.4814-0.78351.37680.0652-0.5582-0.03710.66820.13290.0804-0.3265-0.2890.60490.59750.10360.07630.55810.02430.209635.040633.0066-22.3693
90.84690.5284-0.65090.87340.2650.7773-0.10010.1503-0.2892-0.89210.20610.34420.6942-0.2089-0.00020.6885-0.07650.0640.65710.15870.568927.74563.6532-38.9764
101.08630.7766-0.47821.2111-1.45721.95820.0160.15110.11440.14360.01660.26370.0242-0.230800.42-0.1174-0.03490.44520.09340.680622.12381.1252-28.3046
11-0.8281-0.325-0.37310.4855-0.66160.8862-0.15610.17940.0229-0.48710.18680.06090.3411-0.151-0.00050.4027-0.068-0.02810.38750.15950.492425.54585.3374-34.5153
121.5014-0.335-0.08432.0982-0.97560.8240.0205-0.071-0.11690.32320.0665-0.1144-0.1586-0.07130.00050.46660.05130.02970.46290.02120.271539.869432.7801-36.2572
131.23530.9893-0.59840.3931-0.32231.07040.12480.07560.12740.01030.0781-0.157-0.29510.29660.00040.47520.0158-0.0060.4321-0.02830.383344.612240.4317-38.9474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 358 )A334 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 393 )A359 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 469 )A394 - 469
4X-RAY DIFFRACTION4chain 'A' and (resid 470 through 494 )A470 - 494
5X-RAY DIFFRACTION5chain 'A' and (resid 495 through 527 )A495 - 527
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 119 )H1 - 119
7X-RAY DIFFRACTION7chain 'H' and (resid 120 through 134 )H120 - 134
8X-RAY DIFFRACTION8chain 'H' and (resid 135 through 215 )H135 - 215
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 24 )L1 - 24
10X-RAY DIFFRACTION10chain 'L' and (resid 25 through 61 )L25 - 61
11X-RAY DIFFRACTION11chain 'L' and (resid 62 through 112 )L62 - 112
12X-RAY DIFFRACTION12chain 'L' and (resid 113 through 173 )L113 - 173
13X-RAY DIFFRACTION13chain 'L' and (resid 174 through 213 )L174 - 213

+
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