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- PDB-5ug6: Perforin C2 Domain - T431D -

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Basic information

Entry
Database: PDB / ID: 5ug6
TitlePerforin 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
IODIDE ION / Perforin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,6162
Polymers16,4891
Non-polymers1271
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.774, 66.027, 74.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium iodide, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→49.52 Å / Num. obs: 9857 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 18.98 Å2 / Rsym value: 0.325 / Net I/av σ(I): 1.8 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.117.31.5140.41100
2.11-2.247.21.1220.51100
2.24-2.397.20.8280.71100
2.39-2.587.20.5781.11100
2.58-2.837.10.4131.61100
2.83-3.167.10.2263.11100
3.16-3.6570.1434.81100
3.65-4.476.80.11161100
4.47-6.326.50.0817.11100
6.32-33.0146.10.0984.8199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å33.01 Å
Translation2 Å33.01 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nsj

3nsj


Resolution: 2→33.01 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.222 469 4.78 %RANDOM
Rwork0.191 ---
obs0.192 9810 100 %-
Displacement parametersBiso max: 107.95 Å2 / Biso mean: 24.76 Å2 / Biso min: 9.42 Å2
Baniso -1Baniso -2Baniso -3
1--7.7901 Å20 Å20 Å2
2--6.8878 Å20 Å2
3---0.9023 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 1 70 1027
Biso mean--19.28 32.95 -
Num. residues----123
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d324SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes147HARMONIC5
X-RAY DIFFRACTIONt_it982HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
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_contact1154SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d982HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1333HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion16.79
LS refinement shellResolution: 2→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.225 115 4.26 %
Rwork0.19 2587 -
all0.191 2702 -
obs--99.85 %
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)
17.4925-4.3812.52975.3489-0.79560-0.1963-0.11140.2663-0.06480.1555-0.464-0.08410.22370.04070.04560.0366-0.01780.0786-0.05950.055210.6092-29.1146-9.436
23.0980.81670.9830.6203-0.63732.91560.07470.3139-0.1320.0643-0.11390.202-0.2996-0.10830.03920.02160.00350.0133-0.06950.0315-0.0371-2.7468-10.6473-14.1672
310.0841-7.35422.31065.8572-3.319313.15050.0191.00170.55970.0019-0.511-0.9391-0.46060.72830.49190.0737-0.011-0.04170.06330.04640.156210.0261-16.3372-17.5807
46.1884-2.4642-0.17414.1981-0.3416.01420.08890.3186-0.1956-0.2473-0.07660.301-0.06280.1927-0.01220.1082-0.0143-0.01020.04680.00880.0439-6.6694-11.3153-19.7414
52.9119-1.76970.34492.7029-2.21914.29620.17490.0267-0.2141-0.16880.0347-0.00440.07970.0092-0.20960.136-0.0145-0.01740.0482-0.02110.06229.0783-25.3668-14.2855
62.12792.08712.02741.0415-0.228200.1711-0.13270.09190.2045-0.0039-0.3191-0.47470.2304-0.16720.3205-0.0341-0.15870.14720.00270.199113.9208-22.0329-4.501
72.5884-0.75373.71422.5213-4.07726.3353-0.24860.11980.29450.2973-0.1384-0.2595-0.4131-0.00210.3870.18760.0147-0.02460.08210.02150.10962.8515-6.2083-13.0952
84.4718-4.2025-0.09461.33860.59950-0.1749-0.296-0.09290.35640.25990.0944-0.14460.0378-0.0850.13290.0077-0.02030.0014-0.00220.00870.1379-21.6059-3.5405
92.7552-1.85060.45034.40520.7532.10110.17210.0697-0.18760.1001-0.00180.12350.11230.1154-0.17020.0736-0.02330.0189-0.0150.0006-0.01013.9819-24.7503-5.4289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|410 - A|419 }A410 - 419
2X-RAY DIFFRACTION2{ A|420 - A|442 }A420 - 442
3X-RAY DIFFRACTION3{ A|443 - A|448 }A443 - 448
4X-RAY DIFFRACTION4{ A|449 - A|462 }A449 - 462
5X-RAY DIFFRACTION5{ A|463 - A|470 }A463 - 470
6X-RAY DIFFRACTION6{ A|471 - A|476 }A471 - 476
7X-RAY DIFFRACTION7{ A|477 - A|498 }A477 - 498
8X-RAY DIFFRACTION8{ A|499 - A|510 }A499 - 510
9X-RAY DIFFRACTION9{ A|511 - A|535 }A511 - 535

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