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- PDB-3scl: Crystal structure of spike protein receptor-binding domain from S... -

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Basic information

Entry
Database: PDB / ID: 3scl
TitleCrystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed with human-civet chimeric receptor ACE2
Components
  • Angiotensin-converting enzyme 2 chimera
  • Spike glycoprotein
KeywordsHYDROLASE/VIRAL PROTEIN / beta-sheet / HYDROLASE-VIRAL PROTEIN complex
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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport ...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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / endocytosis involved in viral entry into host cell / cilium / negative regulation of ERK1 and ERK2 cascade / SARS-CoV-1 activates/modulates innate immune responses / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / suppression by virus of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / 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 / zinc ion binding / extracellular region / identical protein binding / membrane / 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 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Spike glycoprotein / Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesPaguma larvata (masked palm civet)
Homo sapiens (human)
SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWu, K. / Peng, G. / Wilken, M. / Geraghty, R. / Li, F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus.
Authors: Wu, K. / Peng, G. / Wilken, M. / Geraghty, R.J. / Li, F.
History
DepositionJun 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Data collection
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 chimera
B: Angiotensin-converting enzyme 2 chimera
E: Spike glycoprotein
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,4508
Polymers182,2484
Non-polymers2024
Water00
1
A: Angiotensin-converting enzyme 2 chimera
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2254
Polymers91,1242
Non-polymers1012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-49 kcal/mol
Surface area33920 Å2
MethodPISA
2
B: Angiotensin-converting enzyme 2 chimera
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2254
Polymers91,1242
Non-polymers1012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.670, 119.523, 113.532
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A19 - 102
2116B19 - 102
1216A290 - 397
2216B290 - 397
1316A417 - 430
2316B417 - 430
1126A103 - 289
2126B103 - 289
1226A398 - 416
2226B398 - 416
1326A431 - 615
2326B431 - 615
1136E323 - 506
2136F323 - 506

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Angiotensin-converting enzyme 2 chimera / ACE2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / ...ACE2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15 / Processed angiotensin-converting enzyme 2


Mass: 69875.344 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paguma larvata (masked palm civet), (gene. exp.) Homo sapiens (human)
Gene: ACE2, UNQ868/PRO1885 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q56NL1, UniProt: Q9BYF1, angiotensin-converting enzyme 2
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein / Spike protein S1


Mass: 21248.811 Da / Num. of mol.: 2 / Fragment: receptor binding domain (UNP residues 324-502)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Sequence detailsCHAINS A AND B ARE CHIMERIC, COMPRISING RESIDUES 19-82 OF UNP Q56NL1 AND RESIDUES 83-615 OF UNP Q9BYF1.

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 8.5
Details: 100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 43744 / Num. obs: 42738 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 66.061 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29178 2066 5 %RANDOM
Rwork0.23881 ---
obs0.24153 39318 94.69 %-
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 max: 140.75 Å2 / Biso mean: 77.41 Å2 / Biso min: 27.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å2-0 Å27.82 Å2
2---1.27 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 3→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12518 0 4 0 12522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.93617542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8651534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.49924.663652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.266152086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21832
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110036
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_it1.0541.57686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.922212420
X-RAY DIFFRACTIONr_scbond_it1.62535206
X-RAY DIFFRACTIONr_scangle_it2.6474.55122
X-RAY DIFFRACTIONr_rigid_bond_restr1.121312892
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1648LOOSE POSITIONAL0.45
1A1648LOOSE THERMAL1.8910
2A3215LOOSE POSITIONAL0.585
2A3215LOOSE THERMAL4.3210
3E1397LOOSE POSITIONAL0.285
3E1397LOOSE THERMAL1.5110
LS refinement shellResolution: 3→3.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.437 248 -
Rwork0.396 5323 -
obs--88.04 %
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)
14.02013.99820.48238.75311.08782.7987-0.5848-0.0689-0.22620.3486-0.4601-0.73040.57090.1221.04480.3767-0.03360.15460.0480.12330.541153.8422-16.2309118.166
21.47070.5791-1.27792.6043-1.33453.19640.20230.08570.44850.6262-0.2229-0.0139-0.6850.24350.02060.3767-0.0505-0.15350.23910.11510.320256.996810.1715117.547
329.9085-9.98251.01856.1728-11.619445.33730.18282.7193-0.9961.7984-0.63110.4687-6.42440.96480.44831.43650.02670.37480.35950.18330.887458.551229.8817105.7759
42.44220.7155-1.84121.112-0.7781.5489-0.5053-0.1863-0.2999-0.14210.0881-0.29640.32810.21490.41730.2380.0882-0.02080.28780.12660.251978.7314-2.0026102.273
50.53720.9304-1.62997.2114-2.45245.7979-0.33830.13240.24620.04751.4208-1.33870.2332-0.458-1.08250.55230.1285-0.19340.551-0.12530.875158.647410.0918104.0942
62.47280.6988-1.63791.1439-0.68941.2244-0.38820.27250.0007-0.1260.259-0.05590.3041-0.16770.12920.25420.015-0.06420.25470.03060.222869.51423.683895.3874
71.4746-1.6859-2.44062.83124.2598.7193-0.00480.41370.1769-0.29110.0605-0.10440.3059-0.6093-0.05570.684-0.23930.20340.81810.21460.260640.739638.642139.3331
82.2266-1.3764-3.062.42192.20134.55720.26320.36340.0232-0.5098-0.1443-0.1807-0.4143-0.2097-0.11890.13630.0093-0.02820.3560.01710.179840.995439.956866.1565
920.09525.447.656323.1386-15.234316.7450.19981.3598-1.0981.49950.1311-0.3006-1.09540.7698-0.33080.28280.08140.11210.171-0.08610.327743.111530.012287.0225
101.1994-0.1042-0.29451.624-1.00941.9130.21550.24250.2463-0.27550.32870.0226-0.181-0.3324-0.54420.303-0.0310.04520.31890.07690.303118.899929.920461.6112
112.5013-2.3343-3.80517.3692.45066.0428-0.1216-0.11280.20450.08440.4637-0.23280.15190.1894-0.34210.0259-0.09360.00990.4835-0.09660.317139.539126.990467.5339
121.16680.281-0.39550.6017-0.69181.0458-0.05570.0582-0.1173-0.26880.18450.01910.1662-0.0841-0.12870.3214-0.03560.01880.2723-0.00560.254627.257721.346865.3917
132.3440.19-1.70064.9749-0.38961.5374-0.00420.25860.03610.11870.03090.2962-0.2827-0.2913-0.02670.26820.0868-0.02850.14710.04740.06930.2956-9.4368130.6257
143.30070.8010.39191.12390.12113.85230.17340.55240.4258-0.1779-0.1792-0.3686-0.16860.11220.00580.48780.06920.37840.24650.27920.536765.727250.23842.1036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 102
2X-RAY DIFFRACTION2A290 - 397
3X-RAY DIFFRACTION3A417 - 430
4X-RAY DIFFRACTION4A103 - 289
5X-RAY DIFFRACTION5A398 - 416
6X-RAY DIFFRACTION6A431 - 615
7X-RAY DIFFRACTION7B19 - 102
8X-RAY DIFFRACTION8B290 - 397
9X-RAY DIFFRACTION9B417 - 430
10X-RAY DIFFRACTION10B103 - 289
11X-RAY DIFFRACTION11B398 - 416
12X-RAY DIFFRACTION12B431 - 615
13X-RAY DIFFRACTION13E324 - 502
14X-RAY DIFFRACTION14F324 - 502

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