[English] 日本語
Yorodumi
- PDB-6atk: Crystal structure of the human coronavirus 229E spike protein rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6atk
TitleCrystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N
Components
  • Aminopeptidase N
  • Spike glycoprotein
KeywordsHydrolase/Viral protein / coronavirus / spike / receptor / Hydrolase-Viral protein complex
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane ...alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane / metallopeptidase activity / signaling receptor activity / virus receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion membrane / proteolysis / extracellular space / extracellular exosome / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Zincin-like fold - #20 / Spike glycoprotein, Alphacoronavirus / Immunoglobulin-like - #1910 / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Zincin-like fold ...Zincin-like fold - #20 / Spike glycoprotein, Alphacoronavirus / Immunoglobulin-like - #1910 / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Aminopeptidase N / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.505 Å
AuthorsWong, A.H. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2017
Title: Receptor-binding loops in alphacoronavirus adaptation and evolution.
Authors: Wong, A.H.M. / Tomlinson, A.C.A. / Zhou, D. / Satkunarajah, M. / Chen, K. / Sharon, C. / Desforges, M. / Talbot, P.J. / Rini, J.M.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminopeptidase N
B: Aminopeptidase N
C: Aminopeptidase N
E: Spike glycoprotein
D: Spike glycoprotein
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,63629
Polymers357,9996
Non-polymers5,63623
Water00
1
A: Aminopeptidase N
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,57511
Polymers119,3332
Non-polymers2,2419
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,35310
Polymers119,3332
Non-polymers2,0208
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aminopeptidase N
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7088
Polymers119,3332
Non-polymers1,3756
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.820, 153.820, 322.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 68 through 889 or resid 899 through 967))
21(chain B and (resid 68 through 889 or resid 899 through 967))
31chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 68 through 889 or resid 899 through 967))A68 - 889
121(chain A and (resid 68 through 889 or resid 899 through 967))A899 - 967
211(chain B and (resid 68 through 889 or resid 899 through 967))B68 - 889
221(chain B and (resid 68 through 889 or resid 899 through 967))B899 - 967
311chain CC68 - 1014

-
Components

#1: Protein Aminopeptidase N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma ...hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 103464.984 Da / Num. of mol.: 3 / Fragment: UNP residues 68-967
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP, APN, CD13, PEPN / Production host: Homo sapiens (human) / References: UniProt: P15144, membrane alanyl aminopeptidase
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 15868.112 Da / Num. of mol.: 3 / Fragment: UNP residues 294-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P15423
#3: 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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 55989 / % possible obs: 99.6 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 3.5→3.6 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5490 / CC1/2: 0.68 / Rpim(I) all: 0.33 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FYQ

4fyq


Resolution: 3.505→49.795 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1991 3.56 %
Rwork0.2444 53996 -
obs0.2452 55987 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.77 Å2 / Biso mean: 96.7655 Å2 / Biso min: 47 Å2
Refinement stepCycle: final / Resolution: 3.505→49.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23307 0 353 0 23660
Biso mean--110.66 --
Num. residues----2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324296
X-RAY DIFFRACTIONf_angle_d0.70133134
X-RAY DIFFRACTIONf_chiral_restr0.0483680
X-RAY DIFFRACTIONf_plane_restr0.0074254
X-RAY DIFFRACTIONf_dihedral_angle_d12.8188836
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13179X-RAY DIFFRACTION2.745TORSIONAL
12B13179X-RAY DIFFRACTION2.745TORSIONAL
13C13179X-RAY DIFFRACTION2.745TORSIONAL
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 (%)
3.5047-3.59240.33821390.314237753914100
3.5924-3.68950.38121380.337538043942100
3.6895-3.7980.32181380.298238323970100
3.798-3.92050.371420.309638193961100
3.9205-4.06060.32591460.282338463992100
4.0606-4.22310.30491390.264837933932100
4.2231-4.41520.25071390.256838543993100
4.4152-4.64780.23821450.22638594004100
4.6478-4.93880.24321430.221738594002100
4.9388-5.31970.27761410.222338684009100
5.3197-5.85430.26741430.234338724015100
5.8543-6.69970.2691460.244639074053100
6.6997-8.43420.21341430.212839324075100
8.4342-49.79990.21731490.20943976412596

+
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