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- PDB-4bik: Structure of a disulfide locked mutant of Intermedilysin with hum... -

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Basic information

Entry
Database: PDB / ID: 4bik
TitleStructure of a disulfide locked mutant of Intermedilysin with human CD59
Components
  • CD59 GLYCOPROTEIN
  • INTERMEDILYSIN
KeywordsIMMUNE SYSTEM / COMPLEMENT / CHOLESTEROL DEPENDENT CYTOTOXIN / MEMBRANE ATTACK COMPLEX
Function / homology
Function and homology information


negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / COPI-mediated anterograde transport / specific granule membrane ...negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / COPI-mediated anterograde transport / specific granule membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / blood coagulation / toxin activity / vesicle / killing of cells of another organism / cell surface receptor signaling pathway / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / host cell plasma membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / Ly-6 antigen / uPA receptor -like domain / Thiol-activated cytolysin C-terminal ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / Ly-6 antigen / uPA receptor -like domain / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / u-PAR/Ly-6 domain / Ly-6 antigen/uPA receptor-like / CD59 / CD59 / Snake toxin-like superfamily / Glutaredoxin / Ribbon / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CD59 glycoprotein / Thiol-activated cytolysin
Similarity search - Component
Biological speciesSTREPTOCOCCUS INTERMEDIUS (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.494 Å
AuthorsJohnson, S. / Brooks, N.J. / Smith, R.A.G. / Lea, S.M. / Bubeck, D.
CitationJournal: Cell Rep. / Year: 2013
Title: Structural Basis for Recognition of the Pore- Forming Toxin Intermedilysin by Human Complement Receptor Cd59
Authors: Johnson, S. / Brooks, N.J. / Smith, R.A.G. / Lea, S.M. / Bubeck, D.
History
DepositionApr 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERMEDILYSIN
B: CD59 GLYCOPROTEIN
C: INTERMEDILYSIN
D: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)136,5234
Polymers136,5234
Non-polymers00
Water00
1
A: INTERMEDILYSIN
B: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)68,2612
Polymers68,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-7.6 kcal/mol
Surface area32780 Å2
MethodPISA
2
C: INTERMEDILYSIN
D: CD59 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)68,2612
Polymers68,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-7.4 kcal/mol
Surface area33000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.400, 101.450, 112.880
Angle α, β, γ (deg.)63.75, 89.95, 90.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1, -0.005, -0.013), (-0.005, -1, -0.014), (-0.013, 0.014, -1)-16.3275, -102.78436, -203.75589
2given(1, -0.005, -0.013), (-0.005, -1, -0.014), (-0.013, 0.014, -1)-16.3275, -102.78436, -203.75589

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Components

#1: Protein INTERMEDILYSIN


Mass: 59056.898 Da / Num. of mol.: 2 / Fragment: RESIDUES 34-532 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS INTERMEDIUS (bacteria) / Plasmid: PTRCHISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 / References: UniProt: Q9LCB8
#2: Protein CD59 GLYCOPROTEIN / 1F5 ANTIGEN / 20 KDA HOMOLOGOUS RESTRICTION FACTOR / HRF-20 / HRF20 / MAC-INHIBITORY PROTEIN / MAC- ...1F5 ANTIGEN / 20 KDA HOMOLOGOUS RESTRICTION FACTOR / HRF-20 / HRF20 / MAC-INHIBITORY PROTEIN / MAC-IP / MEM43 ANTIGEN / MEMBRANE ATTACK COMPLEX INHIBITION FACTOR / MACIF / MEMBRANE INHIBITOR OF REACTIVE LYSIS / MIRL / PROTECTIN / CD59


Mass: 9204.445 Da / Num. of mol.: 2 / Fragment: MATURE POLYPEPTIDE, RESIDUES 26-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET59-06 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): UT5600 (DE3) / References: UniProt: P13987
Sequence detailsSEQUENCE AT THE N-TERMINUS IS THE HIS-TAG AND LINKER FROM THE VECTOR. THERE ARE 2 MUTATIONS T346C ...SEQUENCE AT THE N-TERMINUS IS THE HIS-TAG AND LINKER FROM THE VECTOR. THERE ARE 2 MUTATIONS T346C AND I361C THERE IS AN ADDITIONAL M AT THE N-TERMINUS AND AN ADDITIONAL C AT THE C-TERMINUS

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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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG6000, 0.1 M HEPES PH 7, 0.2 M LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9999
DetectorDate: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.46
ReflectionResolution: 3.49→45.45 Å / Num. obs: 13247 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 129.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 3.49→3.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSXIA2data reduction
AimlessXIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1S3R AND 2UWR

1s3r

2uwr


Resolution: 3.494→45.494 Å / σ(F): 1.98 / Phase error: 25.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2661 673 5.1 %
Rwork0.2118 --
obs0.2032 13247 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103 Å2
Refinement stepCycle: LAST / Resolution: 3.494→45.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8387 0 0 0 8387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048571
X-RAY DIFFRACTIONf_angle_d0.9611611
X-RAY DIFFRACTIONf_dihedral_angle_d13.8093127
X-RAY DIFFRACTIONf_chiral_restr0.0371305
X-RAY DIFFRACTIONf_plane_restr0.0041495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4941-3.76310.26731330.23872500X-RAY DIFFRACTION92
3.7631-4.14030.2791270.22152514X-RAY DIFFRACTION92
4.1403-4.7360.27031280.19292526X-RAY DIFFRACTION91
4.736-5.95410.29271240.17942516X-RAY DIFFRACTION92
5.9541-25.36240.22061350.19072516X-RAY DIFFRACTION90
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)
10.30630.0749-0.44021.7663-0.71420.8787-0.0188-0.2112-0.4151-0.1704-0.0205-0.08450.7807-0.00880.03461.4252-0.0141-0.19910.72170.16721.049224.2709-96.3176-71.2485
20.18390.31730.01170.77020.40990.63750.10870.00330.08030.2916-0.352-0.38320.73470.11650.04550.62630.1179-0.08770.5116-0.01190.774226.3108-58.3167-67.9768
32.41040.65720.32352.6056-0.76112.8022-0.1775-0.02650.0874-0.08820.1281-0.48660.29970.385-0.01880.71480.1637-0.11010.5804-0.0610.791129.4987-68.1746-83.7603
40.31830.30680.2963.08611.32262.0701-0.08550.09330.0681-1.25770.0759-0.1684-0.64260.2399-0.05940.44140.01660.13120.72420.07980.451117.3921-24.0183-88.2239
51.1626-0.15030.1510.0740.03410.8596-0.0355-0.2787-0.02810.0372-0.00190.1838-0.1190.2875-0.009-0.0664-0.0134-0.10410.7494-0.0030.425613.1032-28.0027-63.5109
60.48740.0232-0.14350.0055-0.01580.0355-0.0160.2940.275-0.50870.3-0.3049-0.44380.1220.15692.6499-0.25590.14560.40350.06830.7139.5261-4.9824-133.106
70.4222-0.2747-0.3863.298-0.3970.51850.07510.15510.1164-0.3420.2251-0.0187-0.8388-0.0677-0.15011.2969-0.0672-0.16190.6615-0.05520.472740.4719-42.8092-136.9542
81.57350.3272-0.98175.20110.02171.79870.2914-0.6348-0.0115-0.8888-0.1606-0.8549-0.66610.8228-0.04240.9284-0.1918-0.04220.85310.0460.614843.6354-33.2985-121.0851
92.20210.3782-0.05612.4152-0.33652.59270.4956-0.0349-0.43741.031-0.3752-0.51110.353-0.026-0.13020.7433-0.1462-0.32340.5107-0.06930.48531.811-77.275-117.0423
101.6812-0.3271-0.52530.63830.45791.59520.00610.3047-0.1256-0.159-0.34320.14680.2425-0.11860.18290.1497-0.0120.0690.5309-0.06390.567626.7557-72.9135-141.4384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C AND (RESSEQ 56:76 OR RESSEQ 117:201 OR RESSEQ 258:299 OR RESSEQ 379:399 )
2X-RAY DIFFRACTION2CHAIN C AND (RESSEQ 77:116 OR RESSEQ 400:417 )
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 202:257 OR RESSEQ 300:378 )
4X-RAY DIFFRACTION4CHAIN C AND (RESID 418 THROUGH 528 )
5X-RAY DIFFRACTION5CHAIN D AND (RESID 1 THROUGH 77 )
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 56:76 OR RESSEQ 117:201 OR RESSEQ 258:299 OR RESSEQ 379:399 )
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 77:116 OR RESSEQ 400:417)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 202:257 OR RESSEQ 300:378)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 418 THROUGH 528 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1 THROUGH 77 )

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