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- PDB-6atk: Crystal structure of the human coronavirus 229E spike protein rec... -

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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 NAlanine aminopeptidase
  • Spike glycoproteinSpike protein
KeywordsHydrolase/Viral protein / coronavirus / spike / receptor / Hydrolase-Viral protein complex
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / Metabolism of Angiotensinogen to Angiotensins / aminopeptidase activity / secretory granule membrane / peptide binding / endocytosis involved in viral entry into host cell / metallopeptidase activity ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / Metabolism of Angiotensinogen to Angiotensins / aminopeptidase activity / secretory granule membrane / peptide binding / endocytosis involved in viral entry into host cell / metallopeptidase activity / virus receptor activity / signaling receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cell differentiation / 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
Spike glycoprotein, Alphacoronavirus / Zincin-like fold - #20 / 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 ...Spike glycoprotein, Alphacoronavirus / Zincin-like fold - #20 / 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 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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Components

#1: Protein Aminopeptidase N / Alanine aminopeptidase / 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 / Spike protein / 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 / N-Acetylglucosamine


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

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Experimental details

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Experiment

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

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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

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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

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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

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