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- PDB-3kbh: Crystal structure of NL63 respiratory coronavirus receptor-bindin... -

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Basic information

Entry
Database: PDB / ID: 3kbh
TitleCrystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoprotein
KeywordsHYDROLASE / beta sandwich / Envelope protein / Fusion protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Virion / Virulence / Carboxypeptidase / Cell membrane / Chloride / Metal-binding / Metalloprotease / Protease / Secreted
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 / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / regulation of transmembrane transporter activity / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / apical plasma membrane / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / cell surface / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Coronavirus S1 glycoprotein, central receptor binding domain (RBD) / Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A ...Coronavirus S1 glycoprotein, central receptor binding domain (RBD) / Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsWu, K. / Li, W. / Peng, G. / Li, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor.
Authors: Wu, K. / Li, W. / Peng, G. / Li, F.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Angiotensin-converting enzyme 2
E: Spike glycoprotein
B: Angiotensin-converting enzyme 2
F: Spike glycoprotein
C: Angiotensin-converting enzyme 2
G: Spike glycoprotein
D: Angiotensin-converting enzyme 2
H: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,26124
Polymers336,7228
Non-polymers3,53916
Water00
1
A: Angiotensin-converting enzyme 2
E: Spike glycoprotein
C: Angiotensin-converting enzyme 2
G: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,13112
Polymers168,3614
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-29 kcal/mol
Surface area59420 Å2
MethodPISA
2
B: Angiotensin-converting enzyme 2
F: Spike glycoprotein
D: Angiotensin-converting enzyme 2
H: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,13112
Polymers168,3614
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-29 kcal/mol
Surface area59470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.764, 77.764, 631.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 69153.664 Da / Num. of mol.: 4 / Fragment: residues 19-615
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, spike protein, UNQ868/PRO1885 / Plasmid: pFactbac I / Cell line (production host): SF9 INSECT CELLS / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYF1, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein
Spike glycoprotein / S glycoprotein / Peplomer protein / E2


Mass: 15026.847 Da / Num. of mol.: 4 / Fragment: residues 481-616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus NL63 / Gene: 2, human angiotensin-converting enzyme 2, S / Plasmid: pFactbac I / Cell line (production host): SF9 INSECT CELLS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6Q1S2
#3: 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.: 16
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 protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 6000, 100 mM Na citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.255 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.255 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 54947 / % possible obs: 99 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.076 / Rsym value: 0.135
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.687 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.5.0070refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→49.01 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.88 / SU B: 98.663 / SU ML: 0.692 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.668 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29973 2800 5.1 %RANDOM
Rwork0.26817 ---
obs0.26979 52522 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.249 Å2
Baniso -1Baniso -2Baniso -3
1-6.65 Å20 Å20 Å2
2--6.65 Å20 Å2
3----13.3 Å2
Refinement stepCycle: LAST / Resolution: 3.31→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22800 0 224 0 23024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02223708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9432232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39852788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12824.7281176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.385153832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1161584
X-RAY DIFFRACTIONr_chiral_restr0.1110.23412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2781.514000
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.559222588
X-RAY DIFFRACTIONr_scbond_it1.39339708
X-RAY DIFFRACTIONr_scangle_it2.4564.59644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4868tight positional0.040.05
11B4868tight positional0.040.05
11C4868tight positional0.040.05
11D4868tight positional0.040.05
22E888tight positional0.050.05
22F888tight positional0.050.05
22G888tight positional0.050.05
22H888tight positional0.050.05
11A4868tight thermal0.060.5
11B4868tight thermal0.060.5
11C4868tight thermal0.060.5
11D4868tight thermal0.060.5
22E888tight thermal0.080.5
22F888tight thermal0.080.5
22G888tight thermal0.070.5
22H888tight thermal0.070.5
LS refinement shellResolution: 3.31→3.393 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 196 -
Rwork0.374 3831 -
obs--98.85 %
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)
12.8979-1.1627-1.43261.06030.2796.8007-0.6012-0.2497-0.07970.26470.37340.13880.47010.33510.22780.5249-0.05170.07260.190.08620.39390.833-2.79675.06
22.0322-0.69380.20130.7075-0.08539.1752-0.4412-0.598-0.27020.32460.47270.10880.16340.1104-0.03150.34120.35460.18040.56220.18060.5439-31.151-40.476118.141
31.0461-0.5544-0.09851.98250.28758.88440.46960.34950.0875-0.4328-0.3717-0.22810.08240.1613-0.09790.45420.33040.15350.42840.15370.52821.506-7.766143.18
41.049-1.21440.35022.9883-1.62577.1190.41010.36240.1363-0.2122-0.6574-0.10590.36810.53070.24720.238-0.00170.08970.54290.06350.3932-36.091-39.838186.272
56.53070.9652-4.71162.6584-0.262313.29450.26530.0712-0.0987-0.1418-0.2151-0.1197-0.2130.2175-0.05020.1711-0.0383-0.13240.11970.12740.510523.0420.72732.559
610.7091-3.69374.15093.1008-1.402218.84020.04170.7482-0.3434-0.3994-0.48530.3832-0.3356-2.86810.44360.16590.07880.08420.8016-0.09090.6362-51.634-38.27675.285
73.6942-0.9505-1.94234.16980.944518.1905-0.1021-0.24240.44750.48990.0306-0.4685-2.7921-0.2540.07150.81950.1127-0.03850.18360.03660.6454-0.54912.774186.021
82.86721.22410.94526.1293-3.752412.7233-0.2979-0.331-0.154-0.11290.4778-0.10520.1075-0.2546-0.17990.09930.03260.11760.2455-0.14160.5164-39.574-61.984228.841
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 614
2X-RAY DIFFRACTION1A800 - 801
3X-RAY DIFFRACTION2B19 - 614
4X-RAY DIFFRACTION2B800 - 801
5X-RAY DIFFRACTION3C19 - 614
6X-RAY DIFFRACTION3C800 - 801
7X-RAY DIFFRACTION4D19 - 614
8X-RAY DIFFRACTION4D800 - 801
9X-RAY DIFFRACTION5E482 - 602
10X-RAY DIFFRACTION5E1486 - 1512
11X-RAY DIFFRACTION6F482 - 602
12X-RAY DIFFRACTION6F1486 - 1512
13X-RAY DIFFRACTION7G482 - 602
14X-RAY DIFFRACTION7G1486 - 1512
15X-RAY DIFFRACTION8H482 - 602
16X-RAY DIFFRACTION8H1486 - 1512

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