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- PDB-3sck: Crystal structure of spike protein receptor-binding domain from a... -

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Basic information

Entry
Database: PDB / ID: 3sck
TitleCrystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet 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 / 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 / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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
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 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)182,3888
Polymers182,1864
Non-polymers2024
Water00
1
A: Angiotensin-converting enzyme 2 chimera
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1944
Polymers91,0932
Non-polymers1012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme 2 chimera
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1944
Polymers91,0932
Non-polymers1012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.219, 119.277, 113.236
Angle α, β, γ (deg.)90.00, 92.19, 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: 21217.822 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
Has protein modificationY
Sequence detailsCHAINS A AND B ARE CHIMERIC, COMPRISING RESIDUES 19-82 OF UNP Q56NL1 AND RESIDUES 83-615 OF UNP ...CHAINS A AND B ARE CHIMERIC, COMPRISING RESIDUES 19-82 OF UNP Q56NL1 AND RESIDUES 83-615 OF UNP Q9BYF1. IN CHAINS E AND F, L472P AND D480G ARE NATURAL VARIANTS OF UNP P59594.

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 8.5
Details: 20 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: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 46750 / Num. obs: 42870 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 59.9

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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→47.27 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.896 / SU B: 68.105 / SU ML: 0.516 / Cross valid method: THROUGHOUT / ESU R Free: 0.591 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28529 1723 5.1 %RANDOM
Rwork0.2392 ---
obs0.24157 31946 78.71 %-
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: 162.4 Å2 / Biso mean: 105.24 Å2 / Biso min: 51.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å2-0 Å29.6 Å2
2---2.32 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 3→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12514 0 4 0 12518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212890
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.93617538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.86351534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.1724.585650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.585152084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2921554
X-RAY DIFFRACTIONr_chiral_restr0.0860.21828
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110038
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_it1.1611.57686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.145212420
X-RAY DIFFRACTIONr_scbond_it1.39235204
X-RAY DIFFRACTIONr_scangle_it2.3234.55118
X-RAY DIFFRACTIONr_rigid_bond_restr1.282312890
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 POSITIONAL0.295
1A1648LOOSE THERMAL1.310
2A3215LOOSE POSITIONAL0.595
2A3215LOOSE THERMAL4.6510
3E1395LOOSE POSITIONAL0.165
3E1395LOOSE THERMAL1.310
LS refinement shellResolution: 3→3.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 131 -
Rwork0.398 2440 -
obs--44.59 %
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)
15.10014.86133.21417.91262.34314.5739-0.37110.0713-0.29980.1956-0.0103-0.72310.46450.22050.38130.3930.03740.11260.01790.04130.175653.8967-15.9649118.1001
21.5391.0991-0.72991.741-0.11552.78120.08740.04310.41130.329-0.02770.1018-0.17990.2249-0.05970.26-0.0101-0.05110.16590.07380.281456.7910.3948117.3865
316.0915-7.77042.72125.8224-5.72069.84490.38651.92590.53341.1546-0.5521-0.2525-2.7726-0.42990.16551.04610.1625-0.09960.3570.10450.798658.23130.1332105.4648
42.80270.6732-1.21451.3929-0.74161.1886-0.4872-0.2187-0.1706-0.0340.1095-0.21510.25890.36540.37770.19990.13830.09550.27430.15280.194478.4836-1.8686101.8223
53.42143.7553-3.576120.0427-5.63943.977-0.2501-0.00150.49120.59930.6165-0.56550.0577-0.1382-0.36640.29960.0417-0.26560.33690.07740.323958.406910.2636103.95
62.56170.4436-1.31110.4845-0.35750.9297-0.33530.23860.0609-0.12880.1598-0.05320.3055-0.15190.17550.25810.00670.01370.23340.04610.257369.16543.875895.0227
72.8389-2.0154-1.84142.55832.65735.38150.05820.49670.172-0.54950.1977-0.06460.178-0.3585-0.25590.7607-0.25480.03650.70190.21470.092440.104238.528938.8247
80.7286-0.3904-0.77611.33060.15874.23790.03030.18940.0467-0.30040.0832-0.2457-0.098-0.1148-0.11340.0793-0.03080.06670.28660.05970.197440.846939.95265.7439
95.05632.17311.776112.7815-20.815239.9284-0.20540.2008-0.41130.0625-0.0327-0.3872-0.34480.24250.23810.12660.105-0.09920.1188-0.12280.143943.27230.055986.7483
100.8020.0349-0.09071.3275-0.85431.488-0.08340.118-0.0254-0.21210.32020.12180.0817-0.2714-0.23690.2245-0.0509-0.00440.23780.08850.22318.392729.664360.8867
113.0003-1.98272.91431.80540.060611.26370.4223-0.37150.1804-0.37190.3572-0.3723-0.0464-0.3855-0.77950.2098-0.1207-0.02190.4432-0.05730.216639.147827.086767.1746
121.19270.3861-0.19630.8863-0.84630.9449-0.00480.0557-0.1936-0.14960.17930.05170.1901-0.0737-0.17460.2951-0.02760.01740.2087-0.00290.215326.837521.302764.8504
132.6173-0.1862-1.50653.9687-0.05371.24210.08070.01830.14910.1359-0.12340.4031-0.2912-0.11310.04270.21140.0255-0.06740.1111-0.04170.116630.4415-9.3377130.3988
142.14880.89720.20891.1051-0.00442.77520.08480.36740.1827-0.3103-0.2208-0.30470.06340.08370.13590.38390.07960.29230.41850.26140.340865.082849.960841.433
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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