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- PDB-4y1s: Structural basis for Ca2+-mediated interaction of the perforin C2... -

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Basic information

Entry
Database: PDB / ID: 4y1s
TitleStructural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes
ComponentsPerforin-1
KeywordsIMMUNE SYSTEM / Perforin / C2 domain / Calcium Binding
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: 1.611 Å
AuthorsConroy, P.J. / Yagi, H. / Whisstock, J.C. / Norton, R.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Ca2+-mediated Interaction of the Perforin C2 Domain with Lipid Membranes.
Authors: Yagi, H. / Conroy, P.J. / Leung, E.W. / Law, R.H. / Trapani, J.A. / Voskoboinik, I. / Whisstock, J.C. / Norton, R.S.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Dec 13, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)16,5152
Polymers16,4751
Non-polymers401
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.700, 43.211, 68.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16475.088 Da / Num. of mol.: 1 / Fragment: C2 domain (UNP residues 410-535) / Mutation: W427A, Y430A, Y486A, 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.68 Å3/Da / Density % sol: 26.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 0.2 M NaCl and 20% (w/v) polyethylene glycol 2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953697 Å / Relative weight: 1
ReflectionResolution: 1.611→36.482 Å / Num. obs: 14926 / % possible obs: 99.87 % / Redundancy: 7.1 % / CC1/2: 0.979 / Rmerge(I) obs: 0.2159 / Net I/σ(I): 30.06
Reflection shellResolution: 1.611→1.669 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5473 / Mean I/σ(I) obs: 4.83 / Num. measured obs: 1443 / CC1/2: 0.86 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSJ

3nsj


Resolution: 1.611→36.482 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 755 5.06 %Random Selection
Rwork0.1661 ---
obs0.1671 14925 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.611→36.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 1 134 1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111016
X-RAY DIFFRACTIONf_angle_d1.2861381
X-RAY DIFFRACTIONf_dihedral_angle_d12.311354
X-RAY DIFFRACTIONf_chiral_restr0.07145
X-RAY DIFFRACTIONf_plane_restr0.007185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6111-1.73550.24881410.18662774X-RAY DIFFRACTION99
1.7355-1.91010.21071420.15952789X-RAY DIFFRACTION100
1.9101-2.18650.19891360.14882817X-RAY DIFFRACTION100
2.1865-2.75460.16281670.16842825X-RAY DIFFRACTION100
2.7546-36.49160.17541690.17012965X-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)
13.5305-0.63531.15272.1238-0.06732.4176-0.22140.01380.1535-0.0410.0680.1694-0.0566-0.20980.00220.0537-0.02810.00460.04840.03260.0768-19.73328.7335-16.5774
27.77650.48351.39744.27283.11795.9313-0.0438-0.0036-0.42620.4104-0.2569-0.39920.59330.3694-0.11580.08510.004-0.06810.13780.02580.10782.7366.9463-4.2715
33.0653-0.56161.93241.3319-0.48982.7404-0.14810.02420.14050.1034-0.00240.019-0.070.0830.12990.0753-0.0028-0.01740.04830.00670.0492-10.86314.1571-11.6832
41.1227-0.084-0.61762.8598-0.0011.6837-0.07370.61210.0777-0.08150.01870.20710.03990.21750.07130.0567-0.0110.00280.1450.02880.0653-9.289210.2349-20.5013
56.33873.92710.03732.5486-0.09890.12640.1073-0.42550.30590.2391-0.4941-0.2026-0.57830.70160.15230.1517-0.0828-0.05710.26930.08640.17176.162419.3519-10.4362
63.40240.58941.72571.33810.14731.9071-0.00730.1038-0.0608-0.08880.00930.08410.07190.0049-0.0260.07690.0135-0.00920.0671-0.00770.0921-16.13363.744-17.9231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 410 through 424 )
2X-RAY DIFFRACTION2chain 'A' and (resid 425 through 435 )
3X-RAY DIFFRACTION3chain 'A' and (resid 436 through 470 )
4X-RAY DIFFRACTION4chain 'A' and (resid 471 through 483 )
5X-RAY DIFFRACTION5chain 'A' and (resid 484 through 490 )
6X-RAY DIFFRACTION6chain 'A' and (resid 491 through 535 )

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