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- PDB-8a53: Crystal structure of AtMCA-IIf C147A (metacaspase 9) from Arabido... -

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Basic information

Entry
Database: PDB / ID: 8a53
TitleCrystal structure of AtMCA-IIf C147A (metacaspase 9) from Arabidopsis thaliana
ComponentsMetacaspase-9
KeywordsHYDROLASE / Metacaspase / Cysteine protease / Caspase-hemoglobinase fold / Plant protein
Function / homology
Function and homology information


apoplast / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis
Similarity search - Function
: / : / Caspase domain / Caspase-like domain superfamily
Similarity search - Domain/homology
NITRATE ION / Metacaspase-9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSabljic, I. / Stael, S. / Stahlberg, J. / Bozhkov, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2018.0026 Sweden
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure-function study of a Ca 2+ -independent metacaspase involved in lateral root emergence.
Authors: Stael, S. / Sabljic, I. / Audenaert, D. / Andersson, T. / Tsiatsiani, L. / Kumpf, R.P. / Vidal-Albalat, A. / Lindgren, C. / Vercammen, D. / Jacques, S. / Nguyen, L. / Njo, M. / Fernandez- ...Authors: Stael, S. / Sabljic, I. / Audenaert, D. / Andersson, T. / Tsiatsiani, L. / Kumpf, R.P. / Vidal-Albalat, A. / Lindgren, C. / Vercammen, D. / Jacques, S. / Nguyen, L. / Njo, M. / Fernandez-Fernandez, A.D. / Beunens, T. / Timmerman, E. / Gevaert, K. / Van Montagu, M. / Stahlberg, J. / Bozhkov, P.V. / Linusson, A. / Beeckman, T. / Van Breusegem, F.
History
DepositionJun 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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-9
B: Metacaspase-9
C: Metacaspase-9
D: Metacaspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,6887
Polymers153,5024
Non-polymers1863
Water7,494416
1
A: Metacaspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4382
Polymers38,3761
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metacaspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5003
Polymers38,3761
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metacaspase-9


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metacaspase-9


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.231, 88.143, 82.475
Angle α, β, γ (deg.)90.000, 102.260, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 20 or resid 22...
21(chain B and (resid 7 through 20 or resid 22...
31(chain C and (resid 7 through 20 or resid 22...
41(chain D and (resid 7 through 20 or resid 22...

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
11VALVALPROPRO(chain A and (resid 7 through 20 or resid 22...AA7 - 2030 - 43
12THRTHRGLNGLN(chain A and (resid 7 through 20 or resid 22...AA22 - 4845 - 71
13ASPASPASPASP(chain A and (resid 7 through 20 or resid 22...AA4972
14VALVALPROPRO(chain A and (resid 7 through 20 or resid 22...AA7 - 32530 - 348
15VALVALPROPRO(chain A and (resid 7 through 20 or resid 22...AA7 - 32530 - 348
16VALVALPROPRO(chain A and (resid 7 through 20 or resid 22...AA7 - 32530 - 348
21VALVALPROPRO(chain B and (resid 7 through 20 or resid 22...BB7 - 2030 - 43
22THRTHRGLNGLN(chain B and (resid 7 through 20 or resid 22...BB22 - 4845 - 71
23ASPASPASPASP(chain B and (resid 7 through 20 or resid 22...BB4972
24VALVALPROPRO(chain B and (resid 7 through 20 or resid 22...BB7 - 32530 - 348
25ASPASPASPASP(chain B and (resid 7 through 20 or resid 22...BB5073
31VALVALPROPRO(chain C and (resid 7 through 20 or resid 22...CC7 - 2030 - 43
32THRTHRTHRTHR(chain C and (resid 7 through 20 or resid 22...CC2245
33ARGARGARGARG(chain C and (resid 7 through 20 or resid 22...CC2346
34VALVALPROPRO(chain C and (resid 7 through 20 or resid 22...CC7 - 32530 - 348
35VALVALPROPRO(chain C and (resid 7 through 20 or resid 22...CC7 - 32530 - 348
36VALVALPROPRO(chain C and (resid 7 through 20 or resid 22...CC7 - 32530 - 348
37VALVALPROPRO(chain C and (resid 7 through 20 or resid 22...CC7 - 32530 - 348
41VALVALPROPRO(chain D and (resid 7 through 20 or resid 22...DD7 - 2030 - 43
42THRTHRLYSLYS(chain D and (resid 7 through 20 or resid 22...DD22 - 3745 - 60
43GLUGLUGLUGLU(chain D and (resid 7 through 20 or resid 22...DD3861
44VALVALGLNGLN(chain D and (resid 7 through 20 or resid 22...DD7 - 32430 - 347
45VALVALGLNGLN(chain D and (resid 7 through 20 or resid 22...DD7 - 32430 - 347
46VALVALGLNGLN(chain D and (resid 7 through 20 or resid 22...DD7 - 32430 - 347
47VALVALGLNGLN(chain D and (resid 7 through 20 or resid 22...DD7 - 32430 - 347

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Components

#1: Protein
Metacaspase-9 / AtMC9


Mass: 38375.547 Da / Num. of mol.: 4 / Mutation: G5R, C147A, F271Y
Source method: isolated from a genetically manipulated source
Details: MSYYHHHHHHLESTSLYKKAGST N-terminal expression His-tag and linker G5R cloning artifact C147A engineered mutation F271Y cloning artifact
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AMC9, MCP2F, At5g04200, F21E1.120 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysE
References: UniProt: Q9FYE1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 1.88 Å3/Da / Density % sol: 34.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 14.2 mg/ml in 20 mM Tris/HCl pH 7.4, 100 mM NaCl, Crystallisation condition: 0.2 M Ammonium nitrate pH 6.3, 20% PEG 3350 1 uL protein solution mix with 1 uL crystallisation ...Details: Protein solution: 14.2 mg/ml in 20 mM Tris/HCl pH 7.4, 100 mM NaCl, Crystallisation condition: 0.2 M Ammonium nitrate pH 6.3, 20% PEG 3350 1 uL protein solution mix with 1 uL crystallisation condition and set up against 700 uL crystallisation condition in resorvoir
PH range: 6.3-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→44.38 Å / Num. obs: 81454 / % possible obs: 98.4 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 21.4 / Num. measured all: 580176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-1.997.30.643177443690.9210.2520.6893.296.8
10.13-44.386.60.02402761210.0080.02274.697.9

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSFeb 5, 2021 BUILT=20210205data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 1.95→33.2 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 4078 5.01 %
Rwork0.1737 77265 -
obs0.1755 81343 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.67 Å2 / Biso mean: 45.7227 Å2 / Biso min: 17.17 Å2
Refinement stepCycle: final / Resolution: 1.95→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9205 0 12 416 9633
Biso mean--81.48 45.14 -
Num. residues----1215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5393X-RAY DIFFRACTION8.914TORSIONAL
12B5393X-RAY DIFFRACTION8.914TORSIONAL
13C5393X-RAY DIFFRACTION8.914TORSIONAL
14D5393X-RAY DIFFRACTION8.914TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.9730.27631420.2368261996
1.973-1.9970.23621340.2239262497
1.997-2.02230.25091470.2013259997
2.0223-2.04890.24941540.1992263397
2.0489-2.0770.24641340.1985260897
2.077-2.10660.24671310.1911266298
2.1066-2.13810.25341280.1839263097
2.1381-2.17150.23651490.1898263498
2.1715-2.20710.18771440.179261997
2.2071-2.24510.23681190.1809266398
2.2451-2.28590.24221310.1808266598
2.2859-2.32990.25741150.1807267198
2.3299-2.37740.20571280.1786265998
2.3774-2.42910.20451380.1703266398
2.4291-2.48560.23261460.1806262998
2.4856-2.54770.22561460.1938266698
2.5477-2.61660.22341570.1888265398
2.6166-2.69350.22721270.1874267199
2.6935-2.78040.2331500.189267299
2.7804-2.87980.23961660.1921264699
2.8798-2.9950.23661310.198268999
2.995-3.13120.25611130.1919272399
3.1312-3.29620.23021510.1934269199
3.2962-3.50250.19971690.1844265699
3.5025-3.77250.20341200.1662272299
3.7725-4.15150.16861550.145269499
4.1515-4.75080.16671520.1348270099
4.7508-5.97980.16731660.1607271699
5.9798-33.20.21421350.1658278899
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)
13.0534-0.0394-0.08212.0770.14131.5901-0.03720.09610.3295-0.10030.0364-0.1449-0.04520.08440.0050.1980.0161-0.01720.25620.01160.2775-35.849-3.3539.745
22.65490.0801-0.17292.3597-0.35041.59750.023-0.03460.03570.1868-0.0606-0.1868-0.00630.10070.03360.1905-0.0262-0.00420.2729-0.01760.1955-38.9774.414-32.59
32.27920.12970.22442.04310.02480.9824-0.0240.1120.1066-0.09480.02530.1586-0.027-0.0251-0.00250.20220.01360.00420.23370.00380.19562.9130.29610.236
45.1739-1.0177-0.42081.74020.51732.1182-0.0705-0.2788-0.03380.2216-0.00310.29490.0196-0.26120.03080.2603-0.06130.04320.39880.02120.4083-0.3661.362-31.46
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:325 )A7 - 325
2X-RAY DIFFRACTION2( CHAIN B AND RESID 7:325 )B7 - 325
3X-RAY DIFFRACTION3( CHAIN C AND RESID 7:325 )C7 - 325
4X-RAY DIFFRACTION4( CHAIN D AND RESID 7:324 )D7 - 324

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