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- PDB-4imq: Structural Basis of Substrate Specificity and Protease Inhibition... -

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Basic information

Entry
Database: PDB / ID: 4imq
TitleStructural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus
Components
  • 3C-like protease
  • PEPTIDE INHIBITOR, syc8
Keywordshydrolase/hydrolase inhibitor / Protease / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
peptide inhibitor, syc8 / THIOCYANATE ION / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus Hu/1968/US
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPrasad, B.V.V. / Muhaxhiri, Z. / Deng, L. / Shanker, S. / Sankaran, B. / Estes, M.K. / Palzkill, T. / Song, Y.
CitationJournal: J.Virol. / Year: 2013
Title: Structural basis of substrate specificity and protease inhibition in norwalk virus.
Authors: Muhaxhiri, Z. / Deng, L. / Shanker, S. / Sankaran, B. / Estes, M.K. / Palzkill, T. / Song, Y. / Prasad, B.V.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like protease
B: PEPTIDE INHIBITOR, syc8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9945
Polymers19,8552
Non-polymers1393
Water4,378243
1
A: 3C-like protease
B: PEPTIDE INHIBITOR, syc8
hetero molecules

A: 3C-like protease
B: PEPTIDE INHIBITOR, syc8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,98910
Polymers39,7114
Non-polymers2786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area6020 Å2
ΔGint-47 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.396, 122.396, 51.354
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-493-

HOH

31A-523-

HOH

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Components

#1: Protein 3C-like protease / Genome polyprotein


Mass: 19310.180 Da / Num. of mol.: 1 / Fragment: norwalk virus protease (unp residues 1101-1281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/1968/US / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83883, calicivirin
#2: Protein/peptide PEPTIDE INHIBITOR, syc8


Type: Oligopeptide / Class: Inhibitor / Mass: 545.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: peptide inhibitor, syc8
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNBOUND FORM OF THE PEPTIDE INHIBITOR SYC8 HAD AN ALDEHYDE GROUP THAT UNDERWENT TO REDUCTION ...THE UNBOUND FORM OF THE PEPTIDE INHIBITOR SYC8 HAD AN ALDEHYDE GROUP THAT UNDERWENT TO REDUCTION UPON REACTION WITH CYS 139

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / pH: 7
Details: 0.1-0.3 M potassium, thiocyanate and 25-30%, polyethylene glycol, monomethyl ether 2,000 , pH 7, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2011
RadiationMonochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR. LN2 COOLED FIRST CRYSTAL, SAGITTAL FOCUSING 2ND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 36665 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 15.9 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.5→1.53 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FYQ

2fyq


Resolution: 1.5→31.59 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 1833 5.01 %
Rwork0.17 --
obs0.171 36578 99.7 %
all-36665 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.77 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4279 Å20 Å2-0 Å2
2--0.4279 Å2-0 Å2
3----0.8558 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 7 243 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021416
X-RAY DIFFRACTIONf_angle_d1.6391868
X-RAY DIFFRACTIONf_dihedral_angle_d13.63494
X-RAY DIFFRACTIONf_chiral_restr0.107209
X-RAY DIFFRACTIONf_plane_restr0.01240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5003-1.54090.26531440.242568X-RAY DIFFRACTION98
1.5409-1.58620.21931320.20862646X-RAY DIFFRACTION100
1.5862-1.63740.20991200.17682658X-RAY DIFFRACTION100
1.6374-1.6960.19031390.16562643X-RAY DIFFRACTION100
1.696-1.76390.17741350.1512642X-RAY DIFFRACTION100
1.7639-1.84410.16011490.15352644X-RAY DIFFRACTION100
1.8441-1.94130.19151390.18242617X-RAY DIFFRACTION99
1.9413-2.06290.17921340.16492669X-RAY DIFFRACTION100
2.0629-2.22220.19151470.16562653X-RAY DIFFRACTION100
2.2222-2.44570.18381470.17342670X-RAY DIFFRACTION100
2.4457-2.79950.18981460.17042695X-RAY DIFFRACTION100
2.7995-3.52630.16791530.1642739X-RAY DIFFRACTION100
3.5263-31.59490.1841480.16632901X-RAY DIFFRACTION100
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)
10.7185-0.09960.36080.6495-0.24470.3735-0.0070.0021-0.0316-0.01920.02830.08180.0392-0.0668-0.02010.06840.01330.00420.06280.00710.0575-33.8865-31.4511-3.038
20.80330.19070.91460.40140.73731.75840.0094-0.30830.00360.0214-0.04070.31520.2368-0.7223-0.01560.1109-0.0478-0.05040.16410.01410.1964-44.7909-41.822-7.053
30.82370.13260.39520.39860.28310.59420.01420.0022-0.1669-0.06130.0557-0.09280.09550.0343-0.0750.1297-0.0051-0.01230.0897-0.00640.1088-34.7141-44.4494-5.3478
41.0134-0.0978-0.03820.64470.13120.0617-0.11440.3141-0.0035-0.34110.0737-0.07990.17540.01920.01020.1584-0.0094-0.00830.1244-0.00460.0821-32.8871-33.619-15.2452
50.1955-0.00160.21170.8372-0.15590.1085-0.0084-0.0388-0.07080.10290.0045-0.0225-0.03430.08120.00310.09380.0162-0.00060.09110.01560.0677-27.2075-29.57444.0382
60.1862-0.21570.09660.251-0.01810.17440.0056-0.0288-0.01610.2618-0.06850.0331-0.1165-0.0315-0.02820.10250.0042-0.02730.07640.01920.0662-27.8123-34.802612.5958
70.3306-0.12670.04351.2086-0.02520.8202-0.0721-0.1593-0.07270.0459-0.07450.1962-0.0607-0.16320.01280.1016-0.0085-0.01580.12690.00960.1079-27.8166-39.316912.7211
80.51650.14920.28011.4682-0.06910.9495-0.0020.02040.08080.07750.0353-0.1822-0.09150.05750.03260.08910.01140.00030.0820.01140.0868-27.9529-28.8825.108
90.4621-0.15860.11051.13520.33660.20590.0124-0.05140.03730.11680.0197-0.17930.02390.1207-0.0260.07390.0064-0.00590.09450.0060.0875-26.4795-32.14713.1177
101.4393-1.3219-1.51061.85971.42631.73540.0512-0.30530.12220.4144-0.00920.05840.0915-0.46220.05320.17760.02080.01170.1906-0.02070.0881-30.847-33.165416.5512
113.1930.6104-1.43050.45750.00520.87190.2868-0.7089-0.81670.2315-0.2444-0.11850.17450.91890.03290.21930.0211-0.03740.34570.07180.2757-19.0102-46.17617.4055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:31)
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:43)
3X-RAY DIFFRACTION3chain 'A' and (resseq 44:60)
4X-RAY DIFFRACTION4chain 'A' and (resseq 61:70)
5X-RAY DIFFRACTION5chain 'A' and (resseq 71:93)
6X-RAY DIFFRACTION6chain 'A' and (resseq 94:111)
7X-RAY DIFFRACTION7chain 'A' and (resseq 112:121)
8X-RAY DIFFRACTION8chain 'A' and (resseq 122:149)
9X-RAY DIFFRACTION9chain 'A' and (resseq 150:160)
10X-RAY DIFFRACTION10chain 'A' and (resseq 161:170)
11X-RAY DIFFRACTION11chain 'A' and (resseq 171:181)

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