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- PDB-7roy: The structure of the Fem1B:FNIP1 complex -

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Basic information

Entry
Database: PDB / ID: 7roy
TitleThe structure of the Fem1B:FNIP1 complex
Components
  • Folliculin-interacting protein 1
  • Protein fem-1 homolog B
KeywordsSIGNALING PROTEIN / Complex / Redox sensor / Stress response
Function / homology
Function and homology information


Amino acids regulate mTORC1 / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / positive regulation of B cell apoptotic process / regulation of pro-B cell differentiation / branching involved in prostate gland morphogenesis / immature B cell differentiation / Neddylation / ATPase inhibitor activity / regulation of DNA damage checkpoint ...Amino acids regulate mTORC1 / regulation of ubiquitin-protein transferase activity / epithelial cell maturation involved in prostate gland development / positive regulation of B cell apoptotic process / regulation of pro-B cell differentiation / branching involved in prostate gland morphogenesis / immature B cell differentiation / Neddylation / ATPase inhibitor activity / regulation of DNA damage checkpoint / death receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of TOR signaling / epithelial cell maturation / TOR signaling / positive regulation of TOR signaling / cellular response to starvation / guanyl-nucleotide exchange factor activity / regulation of protein phosphorylation / positive regulation of protein-containing complex assembly / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of peptidyl-serine phosphorylation / protein-folding chaperone binding / protein ubiquitination / positive regulation of protein phosphorylation / lysosomal membrane / apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
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. / Domain of unknown function DUF3447 ...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. / Domain of unknown function DUF3447 / 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
Folliculin-interacting protein 1 / Protein fem-1 homolog B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsGee, C.L. / Mena, E.L. / Manford, A.G. / Rape, M.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Cancer SocietyPF1521501DCC United States
National Science Foundation (NSF, United States) United States
CitationJournal: Cell / Year: 2021
Title: Structural basis and regulation of the reductive stress response.
Authors: Manford, A.G. / Mena, E.L. / Shih, K.Y. / Gee, C.L. / McMinimy, R. / Martinez-Gonzalez, B. / Sherriff, R. / Lew, B. / Zoltek, M. / Rodriguez-Perez, F. / Woldesenbet, M. / Kuriyan, J. / Rape, M.
History
DepositionAug 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
B: Protein fem-1 homolog B
C: Protein fem-1 homolog B
D: Protein fem-1 homolog B
G: Folliculin-interacting protein 1
H: Folliculin-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,93618
Polymers176,4596
Non-polymers1,47612
Water30617
1
A: Protein fem-1 homolog B
D: Protein fem-1 homolog B
G: Folliculin-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9689
Polymers88,2303
Non-polymers7386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein fem-1 homolog B
C: Protein fem-1 homolog B
H: Folliculin-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9689
Polymers88,2303
Non-polymers7386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.475, 164.475, 465.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42

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Components

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fem1b, F1aa, Kiaa0396 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: Q9Z2G0
#2: Protein/peptide Folliculin-interacting protein 1


Mass: 3504.970 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fnip1, Kiaa1961 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: Q68FD7
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.46 Å3/Da / Density % sol: 72.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: FEM1B-FNIP1 complex (20 mg/mL) was mixed in a 1:1 ratio with the reservoir solution containing 6% isopropanol, 150 mM NaCl, and 100 mM HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.194992 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019
Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: Si (111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.194992 Å / Relative weight: 1
ReflectionResolution: 2.9→49.33 Å / Num. obs: 70955 / % possible obs: 100 % / Redundancy: 27.3 % / Biso Wilson estimate: 74.65 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.064 / Rrim(I) all: 0.334 / Rsym value: 0.321 / Χ2: 1.01 / Net I/σ(I): 12.8
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 25.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4478 / CC1/2: 0.452 / Rpim(I) all: 0.979 / Rrim(I) all: 4.993 / Rsym value: 4.776 / Χ2: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
Aimless0.7.4data scaling
CRANK22.0.207phasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.33 Å / SU ML: 0.4521 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 25.736 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 6777 5.01 %
Rwork0.2063 128369 -
obs0.2075 135146 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.85 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12082 0 68 17 12167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001712388
X-RAY DIFFRACTIONf_angle_d0.438716783
X-RAY DIFFRACTIONf_chiral_restr0.03741887
X-RAY DIFFRACTIONf_plane_restr0.00282170
X-RAY DIFFRACTIONf_dihedral_angle_d13.55437440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.930.37842240.364300X-RAY DIFFRACTION100
2.93-2.970.35472180.33764260X-RAY DIFFRACTION99.98
2.97-30.32622400.32444235X-RAY DIFFRACTION100
3-3.040.37472070.32254307X-RAY DIFFRACTION100
3.04-3.080.34132300.3284278X-RAY DIFFRACTION99.96
3.08-3.120.36032330.32624222X-RAY DIFFRACTION100
3.12-3.170.34722450.3234353X-RAY DIFFRACTION100
3.17-3.220.29652420.30294224X-RAY DIFFRACTION100
3.22-3.270.35122200.30644299X-RAY DIFFRACTION99.96
3.27-3.320.31592340.28284258X-RAY DIFFRACTION99.98
3.32-3.380.2952290.27534314X-RAY DIFFRACTION100
3.38-3.440.28492340.2614262X-RAY DIFFRACTION99.89
3.44-3.50.29241980.25174276X-RAY DIFFRACTION99.96
3.5-3.580.28742430.23494301X-RAY DIFFRACTION100
3.58-3.650.24541960.23464272X-RAY DIFFRACTION99.87
3.65-3.740.25122270.22894278X-RAY DIFFRACTION100
3.74-3.830.23132260.20914302X-RAY DIFFRACTION100
3.83-3.940.24262530.19564234X-RAY DIFFRACTION100
3.94-4.050.20382310.19434260X-RAY DIFFRACTION100
4.05-4.180.21962180.17894291X-RAY DIFFRACTION100
4.18-4.330.20592090.16974341X-RAY DIFFRACTION100
4.33-4.50.18192190.16884223X-RAY DIFFRACTION100
4.5-4.710.19262300.1574351X-RAY DIFFRACTION99.98
4.71-4.960.18082330.16034200X-RAY DIFFRACTION99.98
4.96-5.270.1951950.16354336X-RAY DIFFRACTION99.96
5.27-5.670.20612380.17744274X-RAY DIFFRACTION100
5.67-6.240.2252270.19474279X-RAY DIFFRACTION100
6.24-7.150.20092120.17734315X-RAY DIFFRACTION99.96
7.15-8.990.1762460.14464244X-RAY DIFFRACTION100
8.99-49.330.16932200.17864280X-RAY DIFFRACTION99.36

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