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- PDB-2pqr: Crystal structure of yeast Fis1 complexed with a fragment of yeas... -

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Basic information

Entry
Database: PDB / ID: 2pqr
TitleCrystal structure of yeast Fis1 complexed with a fragment of yeast Caf4
Components
  • Mitochondria fission 1 protein
  • WD repeat protein YKR036CWD40 repeat
KeywordsAPOPTOSIS / TPR domain / protein-protein complex
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / CCR4-NOT complex / peroxisome organization / peroxisome fission / mitochondrial fission / positive regulation of mitochondrial fission / preribosome, large subunit precursor / peroxisome / mitochondrial outer membrane / apoptotic process ...Class I peroxisomal membrane protein import / CCR4-NOT complex / peroxisome organization / peroxisome fission / mitochondrial fission / positive regulation of mitochondrial fission / preribosome, large subunit precursor / peroxisome / mitochondrial outer membrane / apoptotic process / regulation of transcription by RNA polymerase II / mitochondrion
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1070 / CCR4-associated factor 4 / CCR4-associated factor 4 / Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat / Fis1 C-terminal tetratricopeptide repeat / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1070 / CCR4-associated factor 4 / CCR4-associated factor 4 / Mitochondria fission 1 protein / Fis1, N-terminal tetratricopeptide repeat / Fis1, C-terminal tetratricopeptide repeat / Mitochondria fission protein Fis1, cytosolic domain / Fis1 N-terminal tetratricopeptide repeat / Fis1 C-terminal tetratricopeptide repeat / : / Tetratricopeptide repeat domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
: / CCR4-associated factor 4 / Mitochondrial fission 1 protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZhang, Y. / Chan, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural basis for recruitment of mitochondrial fission complexes by Fis1.
Authors: Zhang, Y. / Chan, D.C.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondria fission 1 protein
B: Mitochondria fission 1 protein
C: WD repeat protein YKR036C
D: WD repeat protein YKR036C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9466
Polymers44,5534
Non-polymers3942
Water2,540141
1
A: Mitochondria fission 1 protein
C: WD repeat protein YKR036C


Theoretical massNumber of molelcules
Total (without water)22,2762
Polymers22,2762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondria fission 1 protein
D: WD repeat protein YKR036C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6704
Polymers22,2762
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.408, 46.948, 64.468
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL ASSEMBLY IS CONSISTED OF ONE FIS1 AND ONE CAF4 FRAGMENT. THERE ARE TWO BIOLOGICAL UNITS IN ONE ASYMMETRIC UNIT.

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Components

#1: Protein Mitochondria fission 1 protein / Mitochondrial division protein 2


Mass: 15128.260 Da / Num. of mol.: 2 / Fragment: cytoplasmic portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FIS1, MDV2 / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P40515
#2: Protein WD repeat protein YKR036C / WD40 repeat


Mass: 7147.994 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CAF4 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P36130
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 16% PEG3350, 0.2 M NaH2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.90272
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2006
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90272 Å / Relative weight: 1
ReflectionResolution: 1.9→40.4 Å / Num. obs: 56106 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Χ2: 1.104 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.424 / Num. unique all: 5584 / Χ2: 0.919 / % possible all: 98.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å40.41 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2PQN

2pqn


Resolution: 1.88→40.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.548 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1333 4.9 %RANDOM
Rwork0.208 ---
all0.209 ---
obs0.209 27376 92.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.07 Å2
2---0.7 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.88→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 2 141 2651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222574
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9733487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7823.73126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18115457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7061520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021951
X-RAY DIFFRACTIONr_nbd_refined0.2120.21230
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21795
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.27
X-RAY DIFFRACTIONr_mcbond_it0.8241.51598
X-RAY DIFFRACTIONr_mcangle_it1.22622490
X-RAY DIFFRACTIONr_scbond_it2.02231143
X-RAY DIFFRACTIONr_scangle_it2.9784.5994
LS refinement shellResolution: 1.876→1.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 65 -
Rwork0.263 1341 -
obs-1406 65.85 %
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)
14.2225-3.5949-1.4815.85331.6759.8215-0.0265-0.5369-0.8510.36330.954-0.39920.9740.7073-0.9275-0.2447-0.0289-0.0105-0.00440.10740.252636.026-2.0927.283
27.35323.22620.67422.5426-0.09642.8858-0.00720.2939-0.0484-0.13890.34980.38570.038-0.1608-0.3426-0.16240.0031-0.0212-0.03550.03460.093829.153.80119.447
32.02830.837-0.75632.19960.4383.12190.0526-0.12410.13870.21-0.07080.1402-0.12760.02740.01820.08790.00150.0396-0.039-0.0019-0.054254.31515.9324.661
42.14020.5981-0.07852.5085-0.45193.6518-0.02910.10180.06240.01730.0002-0.1036-0.23920.16050.0290.0377-0.02170.0265-0.0224-0.0031-0.07861.43718.40213.411
57.95670.78663.75895.3728-1.39119.4165-0.07010.10080.47410.19220.0121-0.0343-0.5451-0.1010.0580.1381-0.03740.0547-0.04150.0906-0.05559.71330.7576.695
631.0793-0.767-15.30067.07972.884717.1639-0.75062.3806-2.2864-0.587-0.2291-0.4187-0.0333-0.21710.9797-0.2103-0.0191-0.176-0.0124-0.07420.290325.0392.8679.183
714.25711.8689.42594.45490.355315.20650.0835-0.504-0.60870.55620.07050.3013-0.426-0.2596-0.154-0.0206-0.01990.0828-0.05440.0480.064942.8665.66125.697
86.65632.21337.44354.41213.259313.6059-0.17730.3533-0.0503-0.06730.1932-0.5674-0.33970.6757-0.0159-0.02190.00180.03360.0541-0.0417-0.022369.17313.73910.631
96.7116-2.4964-16.044234.9002-7.038843.3337-0.70622.1719-0.2413-2.90481.0508-0.11631.7198-1.9694-0.34460.6104-0.0091-0.1190.9453-0.11290.05145.91712.582.118
104.8635-1.0727-4.49316.9696-2.762812.44020.1434-0.02420.27190.58950.07010.463-0.3173-0.5261-0.21350.00930.01460.0804-0.0596-0.0244-0.009145.41216.62123.043
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 215 - 21
22AA22 - 10222 - 102
33BB5 - 545 - 54
44BB55 - 10355 - 103
55BB104 - 128104 - 128
66CC99 - 12223 - 46
77CC123 - 14047 - 64
88DD96 - 11520 - 39
99DD116 - 12340 - 47
1010DD124 - 13848 - 62

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