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- PDB-3d0i: Crystal structure of spike protein receptor-binding domain from t... -

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Basic information

Entry
Database: PDB / ID: 3d0i
TitleCrystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet 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 / carboxypeptidase activity / negative regulation of signaling receptor activity / viral life cycle / regulation of cytokine production / positive regulation of cardiac muscle contraction / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / endocytosis involved in viral entry into host cell / cilium / 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 / Resolution: 2.9 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: 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 1.3Jun 28, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
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)180,46414
Polymers178,9354
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)90,0116
Polymers89,4672
Non-polymers5434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Angiotensin-converting enzyme 2
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4538
Polymers89,4672
Non-polymers9866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.424, 119.824, 109.772
Angle α, β, γ (deg.)90.00, 95.50, 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 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: 20390.959 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: 2.94 Å3/Da / Density % sol: 58.2 %
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: 2.9→50 Å / Num. obs: 46550

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.9→36.47 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 46.624 / SU ML: 0.387 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2052 5 %RANDOM
Rwork0.224 ---
obs0.227 41328 89.92 %-
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: 84.359 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å24.71 Å2
2--1.06 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12518 0 94 27 12639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212980
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.94417658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.82651534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6924.585650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.918152092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691554
X-RAY DIFFRACTIONr_chiral_restr0.0820.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210054
X-RAY DIFFRACTIONr_nbd_refined0.2630.26913
X-RAY DIFFRACTIONr_nbtor_refined0.3240.28994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2472
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.23
X-RAY DIFFRACTIONr_mcbond_it1.2881.57837
X-RAY DIFFRACTIONr_mcangle_it2.277212410
X-RAY DIFFRACTIONr_scbond_it1.70435979
X-RAY DIFFRACTIONr_scangle_it2.3794.55248
X-RAY DIFFRACTIONr_rigid_bond_restr1.454313816
X-RAY DIFFRACTIONr_sphericity_free4.237331
X-RAY DIFFRACTIONr_sphericity_bonded0.656312608
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1649LOOSE POSITIONAL0.275
1A1649LOOSE THERMAL2.3610
2A3215LOOSE POSITIONAL0.55
2A3215LOOSE THERMAL5.7910
3E1395LOOSE POSITIONAL0.115
3E1395LOOSE THERMAL1.1410
LS refinement shellResolution: 2.9→3.056 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 210 -
Rwork0.322 4593 -
all-4803 -
obs--72.23 %
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)
13.60463.81272.01456.67791.23426.9158-0.74670.0672-0.3293-0.1067-0.2692-0.77460.22790.59251.016-0.0534-0.08960.1415-0.13660.1688-0.067746.4118-16.5002113.0559
21.66550.2409-1.03013.9106-3.49374.54790.2815-0.01710.51461.4411-0.654-0.6841-1.23510.6210.37250.3407-0.3329-0.22310.01310.16570.270451.00739.7024113.1419
311.1302-20.8616-5.672293.9331-25.554637.07351.59350.94451.60462.5086-2.1949-0.9779-2.2521.80570.60150.0025-0.1194-0.06080.06780.15520.062652.723329.5959101.4543
43.39021.3293-2.02081.4381-1.05922.0506-0.4904-0.236-0.2604-0.0642-0.1379-0.18160.40770.41780.62830.02880.1680.1784-0.01890.17180.082571.7736-2.095198.0865
51.64622.4685-2.722227.08-0.87244.94220.0465-0.11690.5865-0.113-0.2026-1.4709-0.49430.27190.1562-0.1488-0.0764-0.25380.04310.24420.41752.17499.982499.8222
63.28571.4879-2.31150.8181-0.99941.7488-0.42350.4420.0492-0.22580.1869-0.07760.3864-0.17270.2366-0.04710.01210.044-0.06740.1113-0.023662.79453.726491.2423
71.593-1.4032-2.0542.05263.37018.9301-0.35450.55120.2979-0.53880.4462-0.11890.6165-0.2372-0.09170.1134-0.31170.00590.18040.1328-0.267437.063338.073536.2304
80.86060.0298-1.06771.02240.63674.1546-0.06830.4296-0.0989-0.29010.0359-0.16280.07990.32390.0324-0.2745-0.0752-0.0464-0.07630.0578-0.168636.263639.946462.8955
99.13741.17326.91652.8269-3.277311.7185-0.9397-0.2718-0.344-0.13410.6074-0.93150.51680.26140.3323-0.2930.2104-0.0885-0.2514-0.0638-0.10837.542230.042483.7277
100.7703-0.08630.2030.8191-0.70031.282-0.05110.01450.0005-0.08090.24110.13560.0846-0.2693-0.19-0.1015-0.0643-0.0366-0.1310.0564-0.051313.96229.443957.8794
110.7648-0.83160.64050.99230.75924.6152-0.44360.1607-0.07440.08150.0614-0.02530.6216-0.23130.3822-0.16620.0265-0.00710.08260.0145-0.082634.397126.992364.3901
121.30850.2691-0.30550.6346-0.52591.055-0.04740.0144-0.1074-0.21840.10210.01110.3108-0.0154-0.0547-0.0053-0.0095-0.0381-0.03280.0066-0.015822.513821.142362.0897
132.1130.5356-2.2483.833-1.04833.18660.08590.27310.14630.20810.10780.1497-0.6107-0.472-0.19370.050.0381-0.0244-0.04850.0443-0.258623.8694-9.4733126.0984
142.97321.31160.57331.061-0.23772.714-0.10220.45640.0108-0.3691-0.1377-0.29150.02550.28190.2399-0.095-0.08590.11310.18260.32220.011661.368649.79239.4329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 102
2X-RAY DIFFRACTION1A616
3X-RAY DIFFRACTION1A901
4X-RAY DIFFRACTION2A290 - 397
5X-RAY DIFFRACTION2A902
6X-RAY DIFFRACTION3A417 - 430
7X-RAY DIFFRACTION4A103 - 289
8X-RAY DIFFRACTION5A398 - 416
9X-RAY DIFFRACTION6A431 - 615
10X-RAY DIFFRACTION7B19 - 102
11X-RAY DIFFRACTION7B901
12X-RAY DIFFRACTION7B902
13X-RAY DIFFRACTION8B290 - 397
14X-RAY DIFFRACTION8B616
15X-RAY DIFFRACTION9B417 - 430
16X-RAY DIFFRACTION10B103 - 289
17X-RAY DIFFRACTION11B398 - 416
18X-RAY DIFFRACTION12B431 - 615
19X-RAY DIFFRACTION13E324 - 502
20X-RAY DIFFRACTION13E91
21X-RAY DIFFRACTION14F324 - 502

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