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- PDB-3d0h: Crystal structure of spike protein receptor-binding domain from t... -

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Basic information

Entry
Database: PDB / ID: 3d0h
TitleCrystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoprotein
KeywordsHYDROLASE / SARS coronavirus / spike protein / receptor-binding domain / RBD / angiotensin-converting enzyme 2 / ACE2 / virus-host interface / host adaptation / cross-species infections / human / palm civet / Carboxypeptidase / Chloride / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Protease / Secreted / Transmembrane / Envelope protein / Host-virus interaction / Lipoprotein / Palmitate / Virion / Virulence
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / 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 ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / 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 / SARS-CoV-1 activates/modulates innate immune responses / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / symbiont-mediated-mediated suppression of host tetherin activity / 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 / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / 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 / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like ...Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Spike glycoprotein / Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesPaguma larvata (masked palm civet)
Homo sapiens (human)
Human SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsLi, F.
CitationJournal: J.Virol. / Year: 2008
Title: Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections
Authors: Li, F.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme 2
E: Spike glycoprotein
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,52414
Polymers178,9954
Non-polymers1,52910
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Angiotensin-converting enzyme 2
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0416
Polymers89,4982
Non-polymers5434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-49 kcal/mol
Surface area33780 Å2
MethodPISA
3
B: Angiotensin-converting enzyme 2
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4838
Polymers89,4982
Non-polymers9866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-39.9 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.352, 119.841, 109.420
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
12A
22B
32A
42B
52A
62B
13E
23F

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLNGLNAA19 - 1021 - 84
211SERSERGLNGLNBB19 - 1021 - 84
321ASNASNASNASNAA290 - 397272 - 379
421ASNASNASNASNBB290 - 397272 - 379
531HISHISGLUGLUAA417 - 430399 - 412
631HISHISGLUGLUBB417 - 430399 - 412
112ASNASNPROPROAA103 - 28985 - 271
212ASNASNPROPROBB103 - 28985 - 271
322GLUGLULYSLYSAA398 - 416380 - 398
422GLUGLULYSLYSBB398 - 416380 - 398
532ASPASPASPASPAA431 - 615413 - 597
632ASPASPASPASPBB431 - 615413 - 597
113PROPROGLUGLUEC324 - 5021 - 179
213PROPROGLUGLUFD324 - 5021 - 179

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 4 molecules ABEF

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


Mass: 69076.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paguma larvata (masked palm civet), (gene. exp.) Homo sapiens (human)
Gene: ACE2, ACE2, UNQ868/PRO1885 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q56NL1, UniProt: Q9BYF1, angiotensin-converting enzyme 2
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 20420.982 Da / Num. of mol.: 2 / Fragment: residues 324-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: S, 2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594

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Sugars , 2 types, 6 molecules

#3: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 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.: 1
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

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3.1→37.5 Å / Num. obs: 38826

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 3.1→37.5 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.857 / SU B: 64.529 / SU ML: 0.493 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1726 5.1 %RANDOM
Rwork0.221 ---
obs0.225 33878 90.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å24.35 Å2
2--0.99 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 94 27 12643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212984
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.94417664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84451534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38624.646650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.757152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5561552
X-RAY DIFFRACTIONr_chiral_restr0.0840.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210052
X-RAY DIFFRACTIONr_nbd_refined0.2590.27047
X-RAY DIFFRACTIONr_nbtor_refined0.3220.28943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2480
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.22
X-RAY DIFFRACTIONr_mcbond_it1.1871.57844
X-RAY DIFFRACTIONr_mcangle_it2.113212416
X-RAY DIFFRACTIONr_scbond_it1.44435993
X-RAY DIFFRACTIONr_scangle_it2.1734.55248
X-RAY DIFFRACTIONr_rigid_bond_restr1.258313837
X-RAY DIFFRACTIONr_sphericity_free4.538331
X-RAY DIFFRACTIONr_sphericity_bonded0.686312612
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1649LOOSE POSITIONAL0.35
1A1649LOOSE THERMAL1.9810
2A3215LOOSE POSITIONAL0.535
2A3215LOOSE THERMAL4.7110
3E1397LOOSE POSITIONAL0.165
3E1397LOOSE THERMAL0.8810
LS refinement shellResolution: 3.1→3.267 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.403 213 -
Rwork0.327 3859 -
all-4072 -
obs--75.3 %
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)
13.58854.47391.5717.91442.16646.1807-0.80190.0909-0.4537-0.0814-0.0914-0.6160.21310.49910.8934-0.1547-0.1160.1694-0.15250.1313-0.056545.7616-16.242112.6592
21.09760.4156-0.73962.8201-2.90265.15060.22140.19520.5411.3836-0.5029-0.4425-1.08890.62130.28150.2613-0.2284-0.18640.00460.18430.22250.40479.8853112.7647
36.5834-8.2592-7.044978.9163-22.280638.18531.00380.53091.17941.6035-1.5705-0.9063-2.11070.29340.56680.0570.0158-0.073-0.01770.11690.213252.057629.8117101.1157
42.96990.7878-1.72231.2491-0.89411.639-0.4946-0.1945-0.25560.0307-0.07-0.09870.3380.40390.56460.01140.14660.1723-0.00050.14810.030971.1196-1.97397.6453
53.85593.8506-2.405917.40493.47774.0512-0.02670.26160.3416-0.9159-0.0902-0.8128-0.31570.16480.1169-0.0829-0.0062-0.17010.0640.30120.182751.552510.145399.3885
63.11150.8418-1.74610.7202-0.70631.3262-0.41520.38470.0011-0.14980.1611-0.04320.3423-0.14660.2541-0.0598-0.00490.0228-0.05530.1-0.041562.15643.79790.8295
71.0016-0.595-1.471.79092.845.6354-0.34540.52250.0729-0.30020.2525-0.06460.5362-0.31650.09290.0355-0.23240.01410.29050.1777-0.159936.544738.168835.9196
81.0667-0.123-1.34221.10891.00083.9795-0.13960.4206-0.0105-0.27140.0291-0.1146-0.04480.25120.1105-0.3103-0.0323-0.048-0.10690.0675-0.158535.638940.061462.5712
94.8121-5.461411.496116.4458-20.247732.5237-1.1622-0.2099-0.54760.4111.04260.09050.60711.42340.1196-0.4210.11080.0407-0.1984-0.0471-0.048336.838130.177683.3021
100.3647-0.15730.3150.8933-0.68521.2297-0.0034-0.0452-0.0176-0.09490.20980.13060.0701-0.1598-0.2064-0.0904-0.0513-0.0098-0.11620.0343-0.079713.459329.478657.4247
111.40510.13080.58740.12831.252812.6117-0.39820.1282-0.3431-0.1928-0.0289-0.15020.82360.25940.4272-0.16230.1053-0.0395-0.02260.027-0.045633.845227.041263.9287
121.09020.3818-0.16720.646-0.5360.7964-0.01670.0421-0.1636-0.22420.1096-0.01110.2723-0.0367-0.0928-0.0157-0.0005-0.0152-0.04120-0.013222.018421.223261.6592
132.32280.4316-2.21663.9249-0.68983.34790.14640.1970.10570.10860.0640.1988-0.5115-0.4138-0.2104-0.02560.0346-0.0322-0.09730.0463-0.233723.2487-9.3436125.6754
142.69620.82661.00181.22660.16783.1005-0.09520.45970.0807-0.1346-0.1214-0.17470.01260.26010.2166-0.1377-0.05080.08110.11850.2935-0.012960.8649.735239.138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 1021 - 84
2X-RAY DIFFRACTION1AE6161
3X-RAY DIFFRACTION1AK9011
4X-RAY DIFFRACTION2AA290 - 397272 - 379
5X-RAY DIFFRACTION2AL9021
6X-RAY DIFFRACTION3AA417 - 430399 - 412
7X-RAY DIFFRACTION4AA103 - 28985 - 271
8X-RAY DIFFRACTION5AA398 - 416380 - 398
9X-RAY DIFFRACTION6AA431 - 615413 - 597
10X-RAY DIFFRACTION6AA546 - 548528 - 530
11X-RAY DIFFRACTION7BB19 - 1021 - 84
12X-RAY DIFFRACTION7BM9011
13X-RAY DIFFRACTION7BN9021
14X-RAY DIFFRACTION8BB290 - 397272 - 379
15X-RAY DIFFRACTION8BB322304
16X-RAY DIFFRACTION9BB417 - 430399 - 412
17X-RAY DIFFRACTION10BB103 - 28985 - 271
18X-RAY DIFFRACTION11BB398 - 416380 - 398
19X-RAY DIFFRACTION12BB431 - 615413 - 597
20X-RAY DIFFRACTION12BG - H617 - 6181
21X-RAY DIFFRACTION13EC324 - 5021 - 179
22X-RAY DIFFRACTION13EI911
23X-RAY DIFFRACTION14FD324 - 5021 - 179
24X-RAY DIFFRACTION14FJ911

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