[English] 日本語
Yorodumi
- PDB-6zlr: Soaking competent crystal form of the SARS-CoV-2 Receptor Binding... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zlr
TitleSoaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex.
Components
  • CR3022 FAB HEAVY CHAIN
  • CR3022 FAB LIGHT CHAIN
  • Spike glycoproteinSpike protein
KeywordsVIRAL PROTEIN / SARS-COV-2 / VIRAL PROTEIN COMPLEX / ANTIBODY
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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
Authorsde Nicola, G.F. / Nichols, C.E.
CitationJournal: Front Pharmacol / Year: 2020
Title: A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface.
Authors: Nichols, C. / Ng, J. / Keshu, A. / Fraternali, F. / De Nicola, G.F.
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
EEE: Spike glycoprotein
HHH: CR3022 FAB HEAVY CHAIN
LLL: CR3022 FAB LIGHT CHAIN
AAA: Spike glycoprotein
BBB: CR3022 FAB HEAVY CHAIN
CCC: CR3022 FAB LIGHT CHAIN
DDD: Spike glycoprotein
FFF: CR3022 FAB HEAVY CHAIN
GGG: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,44712
Polymers221,7839
Non-polymers6643
Water0
1
EEE: Spike glycoprotein
HHH: CR3022 FAB HEAVY CHAIN
LLL: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1494
Polymers73,9283
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-32 kcal/mol
Surface area28560 Å2
MethodPISA
2
AAA: Spike glycoprotein
BBB: CR3022 FAB HEAVY CHAIN
CCC: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1494
Polymers73,9283
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-33 kcal/mol
Surface area28460 Å2
MethodPISA
3
DDD: Spike glycoprotein
FFF: CR3022 FAB HEAVY CHAIN
GGG: CR3022 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1494
Polymers73,9283
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-31 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.130, 207.130, 199.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains E A
22Chains E D
33Chains H B
44Chains H F
55Chains L C
66Chains L G
77Chains A D
88Chains B F
99Chains C G

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

-
Components

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


Mass: 26095.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody CR3022 FAB HEAVY CHAIN


Mass: 23455.420 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CR3022 FAB LIGHT CHAIN


Mass: 24376.963 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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.: 3
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
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.13 Å3/Da / Density % sol: 76.02 % / Description: Thin Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.09→68.028 Å / Num. obs: 72060 / % possible obs: 91.1 % / Redundancy: 4.7 % / CC1/2: 0.933 / Net I/σ(I): 4.6
Reflection shellResolution: 3.09→3.16 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4356 / CC1/2: 0.415 / % possible all: 90.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 3.1→68.028 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.885 / SU B: 19.006 / SU ML: 0.303 / Cross valid method: FREE R-VALUE / ESU R: 0.908 / ESU R Free: 0.375
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2472 3669 5.123 %
Rwork0.2176 67946 -
all0.219 --
obs-71615 90.525 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.063 Å2-0 Å20 Å2
2--0.063 Å20 Å2
3----0.125 Å2
Refinement stepCycle: LAST / Resolution: 3.1→68.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14694 0 42 0 14736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01315134
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713355
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6520619
X-RAY DIFFRACTIONr_angle_other_deg1.2271.57331205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09923.393672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.873152364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111551
X-RAY DIFFRACTIONr_chiral_restr0.0570.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023130
X-RAY DIFFRACTIONr_nbd_refined0.1830.22181
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.212015
X-RAY DIFFRACTIONr_nbtor_refined0.1690.27262
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.210.28
X-RAY DIFFRACTIONr_nbd_other0.1920.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.22
X-RAY DIFFRACTIONr_mcbond_it4.9925.8717635
X-RAY DIFFRACTIONr_mcbond_other4.9925.877634
X-RAY DIFFRACTIONr_mcangle_it8.0478.7929528
X-RAY DIFFRACTIONr_mcangle_other8.0478.7939529
X-RAY DIFFRACTIONr_scbond_it5.1536.2247499
X-RAY DIFFRACTIONr_scbond_other5.1496.2237497
X-RAY DIFFRACTIONr_scangle_it8.2439.15711091
X-RAY DIFFRACTIONr_scangle_other8.2439.15711091
X-RAY DIFFRACTIONr_lrange_it13.544110.05759019
X-RAY DIFFRACTIONr_lrange_other13.544110.05659019
X-RAY DIFFRACTIONr_ncsr_local_group_10.0250.056128
X-RAY DIFFRACTIONr_ncsr_local_group_20.0230.056134
X-RAY DIFFRACTIONr_ncsr_local_group_30.0230.056545
X-RAY DIFFRACTIONr_ncsr_local_group_40.0290.056557
X-RAY DIFFRACTIONr_ncsr_local_group_50.0310.056804
X-RAY DIFFRACTIONr_ncsr_local_group_60.0270.056770
X-RAY DIFFRACTIONr_ncsr_local_group_70.0240.056153
X-RAY DIFFRACTIONr_ncsr_local_group_80.030.056544
X-RAY DIFFRACTIONr_ncsr_local_group_90.0390.056757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.3572910.355035X-RAY DIFFRACTION92.0498
3.18-3.2680.3452390.3194921X-RAY DIFFRACTION91.995
3.268-3.3620.3342570.2994791X-RAY DIFFRACTION92.0664
3.362-3.4660.3072620.2834616X-RAY DIFFRACTION91.8471
3.466-3.5790.3062580.2644498X-RAY DIFFRACTION91.8679
3.579-3.7050.2722660.2464323X-RAY DIFFRACTION91.6883
3.705-3.8450.2821950.234196X-RAY DIFFRACTION91.0052
3.845-4.0010.2521990.2184045X-RAY DIFFRACTION91.1121
4.001-4.1790.2642090.213836X-RAY DIFFRACTION90.8172
4.179-4.3830.1972050.1823671X-RAY DIFFRACTION90.6879
4.383-4.620.1891730.1593529X-RAY DIFFRACTION90.5135
4.62-4.90.1671670.163326X-RAY DIFFRACTION90.422
4.9-5.2380.2111500.1623124X-RAY DIFFRACTION89.6004
5.238-5.6570.181580.1722864X-RAY DIFFRACTION88.804
5.657-6.1960.221590.1762614X-RAY DIFFRACTION88.2559
6.196-6.9260.1941200.1612406X-RAY DIFFRACTION87.7083
6.926-7.9940.1871410.1642111X-RAY DIFFRACTION88.0375
7.994-9.7830.2161060.1741789X-RAY DIFFRACTION87.4078
9.783-13.8050.237820.2071423X-RAY DIFFRACTION86.5938
13.805-68.0280.36320.325828X-RAY DIFFRACTION83.2527

+
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