[English] 日本語
Yorodumi
- PDB-7sn0: Crystal structure of spike protein receptor binding domain of esc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sn0
TitleCrystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2
Components
  • Angiotensin-converting enzyme 2
  • Surface glycoprotein
KeywordsVIRAL PROTEIN / COVID-19 / SARS-CoV-2 / spike protein / neutralization escape mutant / ACE2 / receptor binding
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / regulation of transmembrane transporter activity / brush border membrane / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsPan, J. / Abraham, J. / Clark, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateno grant number United States
CitationJournal: Science / Year: 2022
Title: Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Authors: Katherine G Nabel / Sarah A Clark / Sundaresh Shankar / Junhua Pan / Lars E Clark / Pan Yang / Adrian Coscia / Lindsay G A McKay / Haley H Varnum / Vesna Brusic / Nicole V Tolan / Guohai ...Authors: Katherine G Nabel / Sarah A Clark / Sundaresh Shankar / Junhua Pan / Lars E Clark / Pan Yang / Adrian Coscia / Lindsay G A McKay / Haley H Varnum / Vesna Brusic / Nicole V Tolan / Guohai Zhou / Michaël Desjardins / Sarah E Turbett / Sanjat Kanjilal / Amy C Sherman / Anand Dighe / Regina C LaRocque / Edward T Ryan / Casey Tylek / Joel F Cohen-Solal / Anhdao T Darcy / Davide Tavella / Anca Clabbers / Yao Fan / Anthony Griffiths / Ivan R Correia / Jane Seagal / Lindsey R Baden / Richelle C Charles / Jonathan Abraham /
Abstract: Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we ...Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
History
DepositionOct 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme 2
C: Surface glycoprotein
D: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,11422
Polymers204,0744
Non-polymers13,03918
Water0
1
A: Angiotensin-converting enzyme 2
C: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,55711
Polymers102,0372
Non-polymers6,5209
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme 2
D: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,55711
Polymers102,0372
Non-polymers6,5209
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.709, 104.015, 223.911
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Angiotensin-converting enzyme 2 / / Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related ...Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related carboxypeptidase / ACE-related carboxypeptidase / Metalloprotease MPROT15


Mass: 71828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: amino acids 1-18 are the endogenous signal peptide of human ACE2, 19-615 are human ACE2 residues 19-615, and 616-621 are the C-terminal 6xHistidine-tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Plasmid: pCMV-IRES-puro / Details (production host): Codex BioSolutions
Cell line (production host): HEK-293 (Thermo Fisher Expi293F)
Production host: Homo sapiens (human)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Surface glycoprotein


Mass: 30208.354 Da / Num. of mol.: 2 / Mutation: N440D, T478K, Y489H, Q493K, S494P
Source method: isolated from a genetically manipulated source
Details: variant evolved in immunocompromised patient 146 days post treatment
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Variant: D146 / Plasmid: pHLSec
Cell line (production host): HEK-293T (Thermo Fisher Expi293F)
Production host: Homo sapiens (human) / References: UniProt: A0A7U0MIF7

-
Sugars , 9 types, 14 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1844.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-4[DGlcpNAcb1-2]DManpa1-3[DGalpb1-4DGlcpNAcb1-4DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-1-4-3-1-4/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_d4-f1_f4-g1_h4-i1_i4-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1844.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2[DGalpb1-4DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-1-4-3-1/a4-b1_b4-c1_c3-d1_c6-i1_d2-e1_d4-g1_e4-f1_g4-h1_i2-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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.: 2
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
#9: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d4-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#10: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1682.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-4[DGlcpNAcb1-2]DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-1-4-3-1/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_d4-f1_f4-g1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#13: 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.: 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, 4 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#12: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (v/v) PEG550 MME, 10% (w/v) PEG 20000, 20mM 1,6-Hexanediol, 20mM 1-Butanol, 20mM 1,2-Propanediol, 20mM 2-Propanol, 20mM 1,4-Butanediol, 20mM 1,3-Propanediol, and 0.1M Tris (base) BICINE pH 8.5
PH range: 7.5 - 8.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.06→200 Å / Num. obs: 71067 / % possible obs: 98.9 % / Redundancy: 3.37 % / Biso Wilson estimate: 87.93 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.246 / Rrim(I) all: 0.294 / Χ2: 0.91 / Net I/σ(I): 5.29
Reflection shellResolution: 3.06→3.25 Å / Rmerge(I) obs: 2.286 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 11134 / CC1/2: 0.196 / Rrim(I) all: 2.745 / Χ2: 0.71 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
BUSTER20201211refinement
O15.1.0model building
XDSbuild 20200417data reduction
XDSbuild 20200417data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.08→111.96 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.521
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1846 4.92 %RANDOM
Rwork0.2347 ---
obs0.2372 37515 99.1 %-
Displacement parametersBiso mean: 97.77 Å2
Baniso -1Baniso -2Baniso -3
1--12.1316 Å20 Å20 Å2
2--4.8771 Å20 Å2
3---7.2544 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3.08→111.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12822 0 866 0 13688
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814172HARMONIC2
X-RAY DIFFRACTIONt_angle_deg119389HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4990SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2328HARMONIC5
X-RAY DIFFRACTIONt_it14172HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1974SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact11319SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion20.57
LS refinement shellResolution: 3.08→3.1 Å
RfactorNum. reflection% reflection
Rfree0.3581 45 -
Rwork0.3159 --
obs0.3185 751 94.54 %
Refinement TLS params.

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)
10.94632.9347-1.847612.4419-2.95942.96250.0549-0.31770.0904-0.3177-0.09880.41690.09040.41690.04390.4779-0.0419-0.04080.82470.02080.46518.050321.8666-37.6605
202.6597-2.09590-1.86723.9207-0.08410.0897-0.33090.08970.0025-0.0436-0.3309-0.04360.08160.5517-0.10730.07810.8754-0.04770.442514.708331.8229-25.7176
31.7338-0.007-0.5860.82370.83124.5508-0.10880.46010.27470.46010.03940.76460.27470.76460.06940.49350.0135-0.11230.8488-0.06310.47338.070713.932-4.2744
41.65640.5513-0.52630.3470.15062.52160.12350.4943-0.43290.49430.0426-0.1826-0.4329-0.1826-0.16610.60340.12780.02370.73620.04570.4753-10.431219.944-13.0355
51.51681.5988-0.87612.56670.6472.0414-0.0416-0.1460.3111-0.1460.0176-0.06330.3111-0.06330.0240.7456-0.0637-0.03220.72010.02230.4689-0.6723.5422-36.4036
60.60050.0472-0.44571.9887-0.44382.1116-0.00690.1087-0.32540.10870.1831-0.1229-0.3254-0.1229-0.17630.54320.0632-0.03020.74660.02850.469-8.551318.8869-22.0113
72.31521.99170.43183.6625-0.37750.87670.24490.1251-0.33920.12510.0052-0.6895-0.3392-0.6895-0.25010.52930.15520.10440.8145-0.06890.5052-20.116119.0242-10.1521
81.53110.9497-0.99421.03990.35441.8216-0.0092-0.20210.1007-0.20210.0115-0.11350.1007-0.1135-0.00230.80310.0314-0.05270.63570.060.452126.928456.536-23.6184
91.13310.24280.08530.9592-0.04131.7525-0.0191-0.0981-0.2942-0.0981-0.0724-0.0669-0.2942-0.06690.09160.73040.0318-0.00520.57920.03760.449637.538174.1526-41.4217
102.7781.1699-0.02454.5821-1.29830-0.0542-0.5068-1.0799-0.50680.2284-0.3068-1.0799-0.3068-0.17420.93230.0987-0.19560.55360.17190.264533.386884.5496-56.3688
116.6444-4.54780.04567.3954-9.95170.02840.50980.38910.8670.3891-0.3140.03240.8670.0324-0.19590.4811-0.14830.14810.73620.00230.35820.890411.1726-71.2077
126.70210.0226-9.746317.68733.137227.4052-0.4160.3371.59950.337-0.1491-1.39211.5995-1.39210.5650.59110.0334-0.07780.4674-0.01220.132813.75859.3028-77.336
132.7424-2.107-11.64160.9270.857424.0517-0.5638-1.17361.3051-1.17360.0353-0.13081.3051-0.13080.52840.5881-0.2066-0.13230.76770.10190.62996.035914.2669-81.2258
140-1.80221.590907.38820-0.0021-0.06580.6074-0.0658-0.0709-1.20870.6074-1.20870.0730.7434-0.00960.20130.74710.04090.613813.156518.2852-66.1256
1516.19434.4575-0.86750.73940.50060-0.2467-1.6663-1.3786-1.66630.4832-1.4404-1.3786-1.4404-0.23650.85810.28130.11190.7902-0.02840.48349.154627.1682-63.1318
163.24320.64982.10341.9754-1.06166.4343-0.0879-0.2812-0.0828-0.2812-0.19720.1912-0.08280.19120.28510.6555-0.01640.22130.787-0.09560.388816.577221.6314-62.8111
176.4728-6.60176.259410.5915.82085.60130.231-0.9696-1.4509-0.96960.10210.5168-1.45090.5168-0.3330.943-0.15920.22320.7633-0.10670.371825.309535.5398-50.8015
181.32290.52290.56331.8062-2.307700.1104-0.1252-0.4125-0.12520.14660.0834-0.41250.0834-0.2570.80950.05880.07880.6482-0.01010.432214.486915.1209-68.207
1910.2022-0.5064-8.5437.81558.10943.8201-0.37880.43080.67390.43080.69510.54580.67390.5458-0.31630.6832-0.1183-0.06890.54170.19260.352940.703764.36313.137
2017.35448.72822.05686.50861.308228.8603-0.0489-0.3443-1.3704-0.34430.10141.1471-1.37041.1471-0.05240.36110.2066-0.17270.6079-0.03540.415742.749173.399216.4027
210.22031.7947-9.02318.2918-3.286725.96940.1863-1.26580.8727-1.26580.1199-0.03180.8727-0.0318-0.30610.66760.02450.06960.5618-0.08330.557238.091182.071417.4098
2213.0678-1.8504-6.84555.813411.641600.2866-0.7655-0.3585-0.7655-0.05040.6234-0.35850.6234-0.23620.4571-0.114-0.01950.8310.12170.367633.05270.2646.0035
2312.4631-1.5076.281405.441600.2421-0.0267-1.1669-0.0267-0.2428-1.546-1.1669-1.5460.00070.71340.03210.04250.8848-0.09420.385624.31172.76872.5044
241.49410.0042-0.83674.0021.87515.0693-0.230.2503-0.01210.25030.17490.1784-0.01210.17840.05510.808-0.0386-0.05870.76520.03990.308830.300165.81114.2539
2517.4296-2.77229.34011.4731.216800.3110.78281.30470.7828-0.0372-0.91321.3047-0.9132-0.27380.7401-0.2824-0.0140.9011-0.06410.515716.526352.8923-3.7017
2612.4025-7.2352.768420.83657.215115.9953-0.4617-0.0374-0.3047-0.03740.5679-1.1798-0.3047-1.1798-0.10620.45270.06840.05120.9539-0.01670.34938.818565.3091-8.4265
275.95334.2283.297210.623511.528415.1212-0.5657-0.3765-0.8212-0.3765-0.142-1.519-0.8212-1.5190.70760.62190.0326-0.04880.6573-0.05980.540636.674771.590310.3409
2800.1216-7.09381.39590.33552.10240.0663-0.1958-0.3335-0.19580.88910.6189-0.33350.6189-0.95540.43250.0074-0.01370.9723-0.11590.440134.020176.052329.8879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|19 - A|82 }A19 - 82
2X-RAY DIFFRACTION2{ A|83 - A|129 }A83 - 129
3X-RAY DIFFRACTION3{ A|130 - A|194 }A130 - 194
4X-RAY DIFFRACTION4{ A|195 - A|293 }A195 - 293
5X-RAY DIFFRACTION5{ A|294 - A|387 }A294 - 387
6X-RAY DIFFRACTION6{ A|388 - A|574 }A388 - 574
7X-RAY DIFFRACTION7{ A|575 - A|615 }A575 - 615
8X-RAY DIFFRACTION8{ B|19 - B|129 }B19 - 129
9X-RAY DIFFRACTION9{ B|130 - B|574 }B130 - 574
10X-RAY DIFFRACTION10{ B|575 - B|615 }B575 - 615
11X-RAY DIFFRACTION11{ C|333 - C|353 }C333 - 353
12X-RAY DIFFRACTION12{ C|354 - C|375 }C354 - 375
13X-RAY DIFFRACTION13{ C|376 - C|393 }C376 - 393
14X-RAY DIFFRACTION14{ C|394 - C|409 }C394 - 409
15X-RAY DIFFRACTION15{ C|410 - C|421 }C410 - 421
16X-RAY DIFFRACTION16{ C|422 - C|469 }C422 - 469
17X-RAY DIFFRACTION17{ C|470 - C|494 }C470 - 494
18X-RAY DIFFRACTION18{ C|495 - C|526 }C495 - 526
19X-RAY DIFFRACTION19{ D|333 - D|353 }D333 - 353
20X-RAY DIFFRACTION20{ D|354 - D|375 }D354 - 375
21X-RAY DIFFRACTION21{ D|376 - D|393 }D376 - 393
22X-RAY DIFFRACTION22{ D|394 - D|409 }D394 - 409
23X-RAY DIFFRACTION23{ D|410 - D|421 }D410 - 421
24X-RAY DIFFRACTION24{ D|422 - D|469 }D422 - 469
25X-RAY DIFFRACTION25{ D|470 - D|494 }D470 - 494
26X-RAY DIFFRACTION26{ D|495 - D|506 }D495 - 506
27X-RAY DIFFRACTION27{ D|507 - D|516 }D507 - 516
28X-RAY DIFFRACTION28{ D|517 - D|526 }D517 - 526

+
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