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- PDB-3d0g: Crystal structure of spike protein receptor-binding domain from t... -

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Basic information

Entry
Database: PDB / ID: 3d0g
TitleCrystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoproteinSpike protein
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 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / 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 / 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 / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / cilium / endocytosis involved in viral entry into host cell / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont entry into host cell / membrane raft / apical plasma membrane / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / metal ion binding / 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-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, 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-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, 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 21, 2017Group: Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / software
Item: _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
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

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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)180,52214
Polymers178,9934
Non-polymers1,52910
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.008, 119.762, 108.801
Angle α, β, γ (deg.)90.000, 96.220, 90.000
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 label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERGLNAA19 - 1021 - 84
211SERGLNBB19 - 1021 - 84
321ASNASNAA290 - 397272 - 379
421ASNASNBB290 - 397272 - 379
531HISGLUAA417 - 430399 - 412
631HISGLUBB417 - 430399 - 412
112ASNPROAA103 - 28985 - 271
212ASNPROBB103 - 28985 - 271
322GLULYSAA398 - 416380 - 398
422GLULYSBB398 - 416380 - 398
532ASPASPAA431 - 615413 - 597
632ASPASPBB431 - 615413 - 597
113PROGLUEC324 - 5021 - 179
213PROGLUFD324 - 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 / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 20419.930 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-Acetylglucosamine


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-Acetylglucosamine


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 / Chloride


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


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

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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: 2.9 Å3/Da / Density % sol: 57.51 %
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: 2.8→50 Å / Num. obs: 50660

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
CNSrefinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.14 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 40.387 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2262 5 %RANDOM
Rwork0.214 ---
obs0.217 44939 93.81 %-
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: 74.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å23.72 Å2
2--1.93 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 94 27 12643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212984
X-RAY DIFFRACTIONr_angle_refined_deg1.271.94417668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76551534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65724.663652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.043152090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4611552
X-RAY DIFFRACTIONr_chiral_restr0.090.21860
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210060
X-RAY DIFFRACTIONr_nbd_refined0.2290.26332
X-RAY DIFFRACTIONr_nbtor_refined0.3150.28823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2413
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.21
X-RAY DIFFRACTIONr_mcbond_it1.0311.57862
X-RAY DIFFRACTIONr_mcangle_it1.853212418
X-RAY DIFFRACTIONr_scbond_it1.12635991
X-RAY DIFFRACTIONr_scangle_it1.84.55250
X-RAY DIFFRACTIONr_rigid_bond_restr1.055313853
X-RAY DIFFRACTIONr_sphericity_free5.227331
X-RAY DIFFRACTIONr_sphericity_bonded0.842312612
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1649LOOSE POSITIONAL0.465
1A1649LOOSE THERMAL2.2810
2A3215LOOSE POSITIONAL0.525
2A3215LOOSE THERMAL4.1110
3E1397LOOSE POSITIONAL0.35
3E1397LOOSE THERMAL0.9510
LS refinement shellResolution: 2.8→2.951 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.396 203 -
Rwork0.366 3978 -
all-4181 -
obs--79.62 %
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)
13.37194.8299-0.40836.9709-0.02646.0093-0.6736-0.0849-0.5326-0.0355-0.3486-0.8830.13840.441.0222-0.1764-0.07430.1329-0.18970.1530.023844.7811-16.1212112.0836
22.841.0322-1.45743.8973-3.40063.91270.65390.12080.9511.6622-0.7244-0.2138-1.40160.58890.07050.5051-0.3116-0.0262-0.03860.18590.328449.436710.0579112.5479
337.245811.4006-33.0789117.957-32.919733.91740.60250.8351.16413.48910.28470.513-1.8189-0.9928-0.88730.10470.1124-0.11640.0730.26990.002651.331430.0495100.7746
43.39171.3632-2.09081.4157-0.88291.6429-0.443-0.0305-0.27060.0912-0.0409-0.26290.22710.33260.4840.01050.11910.123-0.03980.1268-0.010670.1701-1.82697.2126
50.37141.2975-1.055919.96130.75464.28110.31210.55720.79320.5587-0.3816-0.3834-0.5239-0.17720.0695-0.12520.0086-0.05520.09980.3540.413350.618510.317199.1267
64.01131.0409-2.48520.8558-0.8061.5841-0.47720.7340.1046-0.12460.34-0.00410.3741-0.32440.1371-0.059-0.03040.04750.04260.1464-0.026461.19083.956590.386
71.3895-0.6797-3.21590.49571.48997.4857-0.49371.29690.5376-0.3460.8059-0.07121.1092-1.1401-0.31220.1338-0.4552-0.03310.73780.2979-0.172536.27737.662235.1818
81.794-0.1657-1.34930.53261.26684.2792-0.10780.68850.0808-0.30350.0817-0.19680.00920.16940.0262-0.2714-0.04370.0164-0.07390.0938-0.15235.04539.741861.7524
94.87720.23349.59033.3421-4.41725.9952-1.0311-0.46850.6216-0.5437-0.0151-0.71021.55290.97211.0462-0.35520.1631-0.0052-0.3973-0.0198-0.255536.129430.139282.7359
100.76120.165-0.25260.6957-0.77731.6116-0.15350.1744-0.0453-0.10080.33920.25550.1874-0.4162-0.1857-0.0594-0.1194-0.04160.01530.0654-0.082112.728429.421156.7808
111.6383-1.1947-0.65110.87220.340918.6684-0.1120.11710.0542-0.16930.1819-0.10190.8125-0.0357-0.07-0.0755-0.07350.13080.02990.0342-0.001933.160926.708263.2822
121.38560.3498-0.23220.764-0.73651.511-0.12720.1153-0.1777-0.29080.1597-0.03250.4467-0.0681-0.03250.0285-0.06390.0161-0.0204-0.0136-0.039121.235221.039161.0365
133.52150.2538-1.96793.3579-0.69453.08870.05140.23970.25110.14190.2810.2558-0.5802-0.6288-0.33240.02370.05440.048-0.03920.1251-0.188722.3902-9.2802125.3217
143.14031.72980.36231.235-0.03852.8584-0.01170.69330.2306-0.0867-0.0018-0.03920.05760.06520.0135-0.1461-0.06420.06920.19450.3605-0.025760.347349.655938.6151
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 DIFFRACTION8BF6161
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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