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- PDB-8uy3: Fem1B with FNIP1 and Tom20 fragment -

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Basic information

Entry
Database: PDB / ID: 8uy3
TitleFem1B with FNIP1 and Tom20 fragment
Components
  • Folliculin-interacting protein 1
  • Mitochondrial import receptor subunit TOM20 homolog
  • Protein fem-1 homolog B
KeywordsPROTEIN BINDING / Fem1B FNP1 ubiquitin / proteasome / reductive stress response / TOM complex electron transport chain mitochondria
Function / homology
Function and homology information


Amino acids regulate mTORC1 / tRNA import into mitochondrion / TOM complex / positive regulation of B cell apoptotic process / mitochondrion targeting sequence binding / epithelial cell maturation involved in prostate gland development / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of pro-B cell differentiation ...Amino acids regulate mTORC1 / tRNA import into mitochondrion / TOM complex / positive regulation of B cell apoptotic process / mitochondrion targeting sequence binding / epithelial cell maturation involved in prostate gland development / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of pro-B cell differentiation / migrasome / negative regulation of lysosome organization / protein import into mitochondrial matrix / protein-transporting ATPase activity / immature B cell differentiation / branching involved in prostate gland morphogenesis / Neddylation / ATPase inhibitor activity / B cell apoptotic process / Mitochondrial protein import / regulation of DNA damage checkpoint / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of TOR signaling / epithelial cell maturation / protein targeting to mitochondrion / Cul2-RING ubiquitin ligase complex / response to muscle activity / protein insertion into mitochondrial outer membrane / TOR signaling / regulation of protein phosphorylation / positive regulation of TOR signaling / ubiquitin-like ligase-substrate adaptor activity / sperm midpiece / positive regulation of TORC1 signaling / enzyme activator activity / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / cell periphery / positive regulation of protein-containing complex assembly / unfolded protein binding / protein-folding chaperone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / Ub-specific processing proteases / protein ubiquitination / lysosomal membrane / negative regulation of cell population proliferation / apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminus / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile. / Protein import receptor MAS20 ...Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminus / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile. / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Mitochondrial import receptor subunit TOM20 homolog / Folliculin-interacting protein 1 / Protein fem-1 homolog B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGee, C.L. / Manford, A.G. / McMinimy, R. / Rape, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2024
Title: Reactive oxygen species control protein degradation at the mitochondrial import gate.
Authors: McMinimy, R. / Manford, A.G. / Gee, C.L. / Chandrasekhar, S. / Mousa, G.A. / Chuang, J. / Phu, L. / Shih, K.Y. / Rose, C.M. / Kuriyan, J. / Bingol, B. / Rape, M.
History
DepositionNov 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fem-1 homolog B
C: Protein fem-1 homolog B
B: Protein fem-1 homolog B
D: Protein fem-1 homolog B
E: Folliculin-interacting protein 1
F: Folliculin-interacting protein 1
J: Mitochondrial import receptor subunit TOM20 homolog
K: Mitochondrial import receptor subunit TOM20 homolog
H: Folliculin-interacting protein 1
I: Folliculin-interacting protein 1
M: Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,61123
Polymers205,56211
Non-polymers1,04912
Water00
1
A: Protein fem-1 homolog B
E: Folliculin-interacting protein 1
J: Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6967
Polymers53,2323
Non-polymers4644
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein fem-1 homolog B
F: Folliculin-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0945
Polymers45,8672
Non-polymers2273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Protein fem-1 homolog B
K: Mitochondrial import receptor subunit TOM20 homolog
H: Folliculin-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4596
Polymers53,2323
Non-polymers2273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein fem-1 homolog B
I: Folliculin-interacting protein 1
M: Mitochondrial import receptor subunit TOM20 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3635
Polymers53,2323
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.715, 183.715, 183.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A" and (resid 3 through 235 or resid 237...
d_2ens_1chain "B" and (resid 3 through 235 or resid 237...
d_3ens_1chain "C" and (resid 3 through 235 or resid 237...
d_4ens_1chain "D" and (resid 3 through 235 or resid 237...
d_1ens_2chain "E" and resid 16 through 29
d_2ens_2chain "F" and resid 13 through 26
d_1ens_3chain "H" and resid 18 through 28
d_2ens_3chain "I"
d_1ens_4chain "J" and (resid 66 through 104 or resid 106 through 126)
d_2ens_4chain "K" and (resid 66 through 104 or resid 106 through 126)
d_3ens_4chain "M"

NCS ensembles :
ID
ens_4
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.990085966522, 0.0274586684137, 0.137752678468), (0.122980772746, -0.304363462536, 0.944583830164), (0.0678638963736, 0.952160125295, 0.297969104719)-51.1939141176, 55.2953611283, -34.6038749275
2given(0.992103824726, -0.0426756922247, 0.117935517373), (-0.118610780042, -0.0136441789195, 0.992847077469), (-0.0407613030043, -0.998995806635, -0.0185982392349)-44.0349558798, 43.46624009, 44.1977644954
3given(-0.989243349496, 0.105246870845, 0.101590804977), (0.129405318073, 0.953469682141, 0.272304661901), (-0.0682045389486, 0.282521966254, -0.956833046801)-100.404801887, 11.3626923288, -8.27509794477
4given(0.989886438386, -0.0593425755421, 0.128853784688), (-0.127368542283, 0.0281811230829, 0.991455031123), (-0.062466739447, -0.997839808301, 0.0203377342162)-43.140539238, 40.9343468159, 43.8254756521
5given(0.999834305161, 0.00470096131771, -0.0175858802958), (0.0173397810789, 0.0480736569754, 0.998693273982), (0.0055402360262, -0.998832730975, 0.0479841777784)-45.0992683096, 44.2023684422, 43.7910230956
6given(-0.986540766137, 0.144004744901, 0.0774593454362), (0.0520477553328, -0.172522545547, 0.983629504663), (0.155010799347, 0.974422190185, 0.162705400531)-53.9685208202, 50.1590953606, -35.6468045866
7given(-0.961713099018, 0.271420835007, 0.0379294806436), (0.274048409124, 0.953595757538, 0.124710066401), (-0.00232048147091, 0.130329818267, -0.991467979229)-104.778624697, 12.2774448918, -3.48221437833

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Components

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Protein , 2 types, 7 molecules ACBDJKM

#1: Protein
Protein fem-1 homolog B / FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic ...FEM1b / FEM1-beta / Fem-1-like death receptor-binding protein alpha / Fem-1-like in apoptotic pathway protein alpha / F1A-alpha / mt-Fem


Mass: 42362.277 Da / Num. of mol.: 4 / Fragment: residues 1-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fem1b, F1aa, Kiaa0396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2G0
#3: Protein Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 7364.442 Da / Num. of mol.: 3 / Fragment: residues 62-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM20, KIAA0016 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15388

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Protein/peptide , 1 types, 4 molecules EFHI

#2: Protein/peptide
Folliculin-interacting protein 1


Mass: 3504.970 Da / Num. of mol.: 4 / Fragment: residues 590-619
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fnip1, Kiaa1961 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68FD7

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Non-polymers , 4 types, 12 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mg/mL protein complex in 50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM TCEP were mixed in a 2:1 ratio with the reservoir solution containing 30% PEG 3350, 0.2M Ammonium Citrate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.2→49.1 Å / Num. obs: 31515 / % possible obs: 91.7 % / Redundancy: 20.1 % / Biso Wilson estimate: 98.08 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.124 / Rrim(I) all: 0.403 / Rsym value: 0.384 / Χ2: 0.99 / Net I/σ(I): 8.8
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 4.283 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4939 / CC1/2: 0.383 / Rpim(I) all: 1.415 / Rrim(I) all: 4.513

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→45.93 Å / SU ML: 0.5137 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 1579 5.03 %
Rwork0.2391 29809 -
obs0.2404 31388 91.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.03 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13694 0 38 0 13732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002313984
X-RAY DIFFRACTIONf_angle_d0.527718957
X-RAY DIFFRACTIONf_chiral_restr0.03692148
X-RAY DIFFRACTIONf_plane_restr0.00372461
X-RAY DIFFRACTIONf_dihedral_angle_d12.51135130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.40811370.35642905X-RAY DIFFRACTION99.25
3.3-3.420.32661510.3392922X-RAY DIFFRACTION98.59
3.42-3.560.3335770.33161806X-RAY DIFFRACTION61.02
3.56-3.720.32551320.30322011X-RAY DIFFRACTION69.53
3.72-3.880.36771160.29162502X-RAY DIFFRACTION98.94
3.93-4.160.27471580.24952680X-RAY DIFFRACTION97.9
4.16-4.480.28241630.2392986X-RAY DIFFRACTION100
4.48-4.930.24491400.22812943X-RAY DIFFRACTION100
4.93-5.650.29551990.22882950X-RAY DIFFRACTION99.97
5.65-7.10.29171320.22813014X-RAY DIFFRACTION100
7.11-45.930.17781740.18273090X-RAY DIFFRACTION99.91

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