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- PDB-5ug7: Calcium bound Perforin C2 Domain - T431D -

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Basic information

Entry
Database: PDB / ID: 5ug7
TitleCalcium bound Perforin C2 Domain - T431D
ComponentsPerforin-1
KeywordsAPOPTOSIS / C2 / perforin / calcium / proteostasis
Function / homology
Function and homology information


immune response to tumor cell / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / pore-forming activity / protein transmembrane transport / immunological synapse formation / wide pore channel activity / positive regulation of killing of cells of another organism / protein import / defense response to tumor cell ...immune response to tumor cell / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / pore-forming activity / protein transmembrane transport / immunological synapse formation / wide pore channel activity / positive regulation of killing of cells of another organism / protein import / defense response to tumor cell / immunological synapse / protein secretion / endosome lumen / protein homooligomerization / T cell mediated cytotoxicity / circadian rhythm / cytoplasmic vesicle / defense response to virus / killing of cells of another organism / calcium ion binding / extracellular space / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Perforin-1, C2 domain / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) ...Perforin-1, C2 domain / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLaw, R.H.P. / Conroy, P.J. / Voskoboinik, I. / Whisstock, J.C.
CitationJournal: Cell Death Differ. / Year: 2018
Title: Perforin proteostasis is regulated through its C2 domain: supra-physiological cell death mediated by T431D-perforin.
Authors: Brennan, A.J. / Law, R.H.P. / Conroy, P.J. / Noori, T. / Lukoyanova, N. / Saibil, H. / Yagita, H. / Ciccone, A. / Verschoor, S. / Whisstock, J.C. / Trapani, J.A. / Voskoboinik, I.
History
DepositionJan 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 4, 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
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Perforin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6094
Polymers16,4891
Non-polymers1203
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.996, 31.312, 86.364
Angle α, β, γ (deg.)90.000, 101.350, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Perforin-1 / P1 / Cytolysin / Lymphocyte pore-forming protein


Mass: 16489.074 Da / Num. of mol.: 1 / Fragment: C2 Domain (UNP residues 410-535) / Mutation: T431D, W427A, Y430A, Y886A, W488A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prf1, Pfp / Plasmid: pComb3x / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10F' / References: UniProt: P10820
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MgCl2, 0.1 M Na-HEPES pH7.5, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→42.34 Å / Num. obs: 12655 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Net I/σ(I): 17.7 / Num. measured all: 51689 / Scaling rejects: 26
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.833.50.490.86188.6
8.99-42.343.50.0350.996199

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSJ

3nsj


Resolution: 1.8→42.34 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.912 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.233 626 4.95 %RANDOM
Rwork0.211 ---
obs0.212 12635 99.7 %-
Displacement parametersBiso max: 84.23 Å2 / Biso mean: 30.63 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-9.7576 Å20 Å22.6284 Å2
2---1.7196 Å20 Å2
3----8.0379 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.8→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 3 90 1073
Biso mean--18.99 35.59 -
Num. residues----126
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d334SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes151HARMONIC5
X-RAY DIFFRACTIONt_it1007HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion121SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1124SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1007HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1369HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion15.24
LS refinement shellResolution: 1.8→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 145 4.88 %
Rwork0.183 2829 -
all0.185 2974 -
obs--98.94 %
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)
11.28320.6711-0.09510.71960.0410.5445-0.07550.26920.2189-0.01140.03260.0350.0184-0.15740.04290.0726-0.0073-0.02340.09780.00540.094321.709527.754413.2769
25.5662-2.1993-4.16162.894-0.45739.52880.18640.4185-0.1643-0.7406-0.31630.7710.63830.27680.12990.2632-0.0327-0.13720.2940.0070.162918.832223.67413.6434
33.55161.7167-0.111.96930.5730.7788-0.27160.62650.3535-0.23980.15490.0491-0.0945-0.02690.11670.1702-0.012-0.02880.16040.04190.166123.07431.42859.9939
43.6729-2.3076-1.12090-2.5284-0.5980.47020.2746-0.2964-0.3804-0.28750.19970.3819-0.5688-0.18280.337-0.0901-0.07890.40210.02620.19935.475520.35689.7814
57.8133-2.33774.00392.2192-1.27561.29260.0284-0.0189-0.5058-0.31710.05080.08920.2418-0.1144-0.07920.1236-0.0297-0.00880.0499-0.02470.10428.220820.683611.894
610.1883-1.25630.05220.25290.2088-0.38950.1074-0.2189-0.54630.106-0.00470.18760.075-0.5511-0.10270.1954-0.0424-0.0230.23570.01650.250521.744220.360917.3012
78.01841.62042.73430-0.48271.63650.0729-0.1246-0.05170.13370.02410.21520.1089-0.7041-0.0970.09930.0306-0.01230.20830.01460.217510.670629.556918.8106
89.435-0.14196.08950-0.52785.4986-0.2008-0.22230.24030.00610.07-0.01230.0405-0.53930.13080.07510.0097-0.00890.1180.00370.148216.108129.250317.7916
98.41973.6911-2.50355.9988-1.06694.1039-0.06960.34350.4309-0.06010.1116-0.11610.0475-0.6656-0.0420.0720.0085-0.01270.44380.03450.1582-4.251728.86759.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|410 - A|442 }A410 - 442
2X-RAY DIFFRACTION2{ A|443 - A|448 }A443 - 448
3X-RAY DIFFRACTION3{ A|449 - A|470 }A449 - 470
4X-RAY DIFFRACTION4{ A|471 - A|476 }A471 - 476
5X-RAY DIFFRACTION5{ A|477 - A|490 }A477 - 490
6X-RAY DIFFRACTION6{ A|491 - A|498 }A491 - 498
7X-RAY DIFFRACTION7{ A|499 - A|510 }A499 - 510
8X-RAY DIFFRACTION8{ A|511 - A|524 }A511 - 524
9X-RAY DIFFRACTION9{ A|525 - A|535 }A525 - 535

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