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- PDB-6w8r: Crystal structure of metacaspase 4 C139A from Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 6w8r
TitleCrystal structure of metacaspase 4 C139A from Arabidopsis
ComponentsMetacaspase-4
KeywordsPLANT PROTEIN / HYDROLASE / metacaspase / protease / Ca2+-dependent activation / C139A mutant / plant immunity
Function / homology
Function and homology information


plasmodesma / positive regulation of programmed cell death / protein autoprocessing / cysteine-type peptidase activity / defense response / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / mitochondrion / identical protein binding / plasma membrane ...plasmodesma / positive regulation of programmed cell death / protein autoprocessing / cysteine-type peptidase activity / defense response / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / mitochondrion / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.801 Å
AuthorsZhu, P. / Yu, X.H. / Wang, C. / Zhang, Q. / Liu, W. / McSweeney, S. / Shanklin, J. / Lam, E. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for Ca2+-dependent activation of a plant metacaspase.
Authors: Zhu, P. / Yu, X.H. / Wang, C. / Zhang, Q. / Liu, W. / McSweeney, S. / Shanklin, J. / Lam, E. / Liu, Q.
History
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metacaspase-4
B: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5933
Polymers94,4972
Non-polymers961
Water30617
1
A: Metacaspase-4


Theoretical massNumber of molelcules
Total (without water)47,2491
Polymers47,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metacaspase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3452
Polymers47,2491
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.160, 216.100, 40.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:19 or resseq 21:36 or (resid...
21(chain B and (resseq 2:19 or resseq 21:36 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA2 - 192 - 19
12GLYGLYARGARG(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA21 - 3621 - 36
13TYRTYRTYRTYR(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA3737
14METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
15METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
16METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
17METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
18METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
19METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
110METMETALAALA(chain A and (resseq 2:19 or resseq 21:36 or (resid...AA1 - 4241 - 424
21THRTHRLEULEU(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 192 - 19
22GLYGLYARGARG(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB21 - 3621 - 36
23TYRTYRTYRTYR(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB3737
24THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423
25THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423
26THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423
27THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423
28THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423
29THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423
210THRTHRALAALA(chain B and (resseq 2:19 or resseq 21:36 or (resid...BB2 - 4232 - 423

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Components

#1: Protein Metacaspase-4 / AtMC4 / Metacaspase 2d / AtMCP2d / Metacaspase-7


Mass: 47248.559 Da / Num. of mol.: 2 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AMC4, AMC7, MCP2D, At1g79340, YUP8H12R.4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O64517, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, pH 4.6, 2.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.28 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 24420 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.982 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 1779 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.801→39.797 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.266 980 4.97 %
Rwork0.2479 --
obs0.2488 19721 81 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 192.43 Å2 / Biso mean: 36.4259 Å2 / Biso min: 10.53 Å2
Refinement stepCycle: final / Resolution: 2.801→39.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5392 0 5 17 5414
Biso mean--54.65 23.33 -
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045471
X-RAY DIFFRACTIONf_angle_d0.7417379
X-RAY DIFFRACTIONf_dihedral_angle_d15.4193355
X-RAY DIFFRACTIONf_chiral_restr0.046830
X-RAY DIFFRACTIONf_plane_restr0.004983
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3145X-RAY DIFFRACTION6.341TORSIONAL
12B3145X-RAY DIFFRACTION6.341TORSIONAL
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)
11.7813-0.8292-0.17573.17310.08511.20580.066-0.0466-0.056-0.0609-0.1478-0.0070.0706-0.1034-0.00050.0914-0.0093-0.01520.1146-0.01750.103329.4614.0417.818
21.03311.06650.21031.42170.55991.76280.07390.42180.2472-0.342-0.13620.1465-0.1391-0.10890.03170.40460.1573-0.16390.20590.05860.21329.29316.067-2.549
31.28940.02120.76370.0998-0.05450.6952-0.00590.0748-0.1235-0.02290.14530.05470.09220.0527-0.18640.19760.003-0.14790.33520.03820.766847.0827.166.833
41.27261.0567-0.03122.66840.21491.48120.1912-0.1774-0.26280.16390.0081-0.76820.59760.0932-0.08660.25840.1098-0.06490.2615-0.01280.195138.163-3.2048.446
52.00082.5104-1.25368.9256-8.14537.54880.5553.8925-2.8766-2.6263-1.0717-0.44741.3221-0.22180.88050.68660.43890.1431.2563-0.22151.064144.638-16.011-1.546
64.0065-1.01830.592.8262-2.05675.0994-0.04150.18190.01-0.6302-0.19650.38430.0828-0.24940.0230.31540.0783-0.07690.132-0.06490.224431.962-13.4622.105
77.82350.2426-1.38580.1370.22680.80460.2210.69380.6373-1.149-0.5976-0.6273-0.16430.14290.15190.52310.04590.14780.2490.07650.300237.6451.761-7.705
82.26030.14171.37721.5941-0.17694.10080.17520.0320.0463-0.0261-0.1327-0.2278-0.3890.40960.01820.1770.06630.00480.19410.03790.240837.46224.8825.575
93.0014-1.5563-4.11381.85393.38358.22220.47870.03790.9521-0.3483-0.12430.2442-1.4902-1.19-0.32920.40120.0804-0.03440.4380.03270.345531.45735.476-3.536
101.9386-0.33530.79781.7281-0.53962.56940.16860.15750.2366-0.2699-0.2875-0.1877-0.46760.24140.27710.35780.1145-0.0270.14110.09070.256435.73629.997-1.744
111.1739-0.42650.2222.87210.69821.92540.1550.0238-0.17610.4466-0.09370.07910.06860.1805-0.03350.24010.0420.0010.17120.04360.097418.49547.53230.235
121.0484-0.61851.18653.1016-2.63422.91650.30050.06470.1712-0.3209-0.21750.28580.2074-0.2934-0.04710.24530.07350.08960.222-0.02730.24997.87867.4521.658
131.419-1.953-1.01253.06171.50271.00150.0790.53220.0951-0.2477-0.319-0.06820.14990.0622-0.23190.08530.03970.07020.3429-0.0640.161619.21554.46916.321
141.0993-1.2172-0.40334.03540.60183.1454-0.21670.06790.2643-0.2044-0.34340.5437-0.3171-0.5294-0.04830.29760.0752-0.13770.1941-0.01730.29538.33551.24617.421
150.30750.2725-0.36690.74210.07630.86330.0378-0.03140.13310.54070.03830.5872-0.0659-0.0891-0.24940.19980.10440.42040.1444-0.08350.06511.50770.2427.445
167.73817.03757.57712.000229.7765-0.35574.4662.9837-5.17670.702-0.9293-2.58841.4067-0.3791.56790.26560.08771.3943-0.08481.601610.24387.91514.853
171.8489-0.6773-0.19623.27211.17962.7013-0.15260.06360.299-0.4906-0.1737-0.3451-0.09090.0865-0.04530.2145-0.01220.0510.0895-0.05190.290417.78279.37621.197
182.1683-0.1848-1.09191.7602-0.04982.58990.32140.2019-0.19310.2172-0.36440.8034-0.0999-0.31750.0670.29530.01530.07390.1926-0.07470.38555.29242.17322.444
193.1120.7352-3.61921.6588-0.16294.5320.00540.4884-0.1014-0.0311-0.06390.0157-0.0148-0.5927-0.16040.42040.02490.35930.4228-0.06660.848-4.18344.0725.12
204.4566-2.3869-0.08082.89261.07981.00590.01790.1097-0.31890.1516-0.0729-0.1752-0.02590.0695-0.02230.23310.11730.04580.2529-0.06940.320813.80237.66613.897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:120 )A1 - 120
2X-RAY DIFFRACTION2( CHAIN A AND RESID 121:145 )A121 - 145
3X-RAY DIFFRACTION3( CHAIN A AND RESID 146:221 )A146 - 221
4X-RAY DIFFRACTION4( CHAIN A AND RESID 222:279 )A222 - 279
5X-RAY DIFFRACTION5( CHAIN A AND RESID 280:291 )A280 - 291
6X-RAY DIFFRACTION6( CHAIN A AND RESID 292:322 )A292 - 322
7X-RAY DIFFRACTION7( CHAIN A AND RESID 323:329 )A323 - 329
8X-RAY DIFFRACTION8( CHAIN A AND RESID 330:377 )A330 - 377
9X-RAY DIFFRACTION9( CHAIN A AND RESID 378:385 )A378 - 385
10X-RAY DIFFRACTION10( CHAIN A AND RESID 386:424 )A386 - 424
11X-RAY DIFFRACTION11( CHAIN B AND RESID 2:86 )B2 - 86
12X-RAY DIFFRACTION12( CHAIN B AND RESID 87:112 )B87 - 112
13X-RAY DIFFRACTION13( CHAIN B AND RESID 113:131 )B113 - 131
14X-RAY DIFFRACTION14( CHAIN B AND RESID 132:149 )B132 - 149
15X-RAY DIFFRACTION15( CHAIN B AND RESID 150:279 )B150 - 279
16X-RAY DIFFRACTION16( CHAIN B AND RESID 280:286 )B280 - 286
17X-RAY DIFFRACTION17( CHAIN B AND RESID 287:326 )B287 - 326
18X-RAY DIFFRACTION18( CHAIN B AND RESID 327:396 )B327 - 396
19X-RAY DIFFRACTION19( CHAIN B AND RESID 397:402 )B397 - 402
20X-RAY DIFFRACTION20( CHAIN B AND RESID 403:423 )B403 - 423

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