SAXSdb — 8yfk

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1. Protein Identity and Related Structures Protein Identity & Related Structures

RB1-inducible coiled-coil protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1490–1594	Fragment：claw domain	TNIP1_FIR_pS123 peptide × 1 （Q15025） MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 1490–1594	Fragment：claw domain	TNIP1_FIR_pS123 peptide × 1 （Q15025） MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1490–1594	Fragment：claw domain	TNIP1_FIR_pS123 peptide × 1 （Q15025） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1490–1594	Fragment：claw domain	TNIP1_FIR_pS123 peptide × 1 （Q15025） MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8YFK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6DCE X-ray structure of FIP200 claw domain Deposited 2018-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1494–1594（101 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M HEPES pH 7.4, 2 M Ammonium sulfate	Resolution 1.56 Å R-free 0.241
6GMA Crystal structure of the FIP200 C-terminal region Deposited 2018-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1458–1594（137 aa） Chain B 1458–1594（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH 6.0, 1.0 M LiCl, 14% PEG 6000	Resolution 3.20 Å R-free 0.295
6GMA Crystal structure of the FIP200 C-terminal region Deposited 2018-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1458–1594（137 aa） Chain D 1458–1594（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH 6.0, 1.0 M LiCl, 14% PEG 6000	Resolution 3.20 Å R-free 0.295
6GMA Crystal structure of the FIP200 C-terminal region Deposited 2018-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1458–1594（137 aa） Chain F 1458–1594（137 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH 6.0, 1.0 M LiCl, 14% PEG 6000	Resolution 3.20 Å R-free 0.295
7CZG Crystal structure of FIP200 Claw domain apo form Deposited 2020-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1490–1594（105 aa） Chain C 1490–1594（105 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium citrate tribasic dihydrate pH 5.0, Jeffamine ED-2001 pH 7.0	Resolution 1.80 Å R-free 0.230
7CZG Crystal structure of FIP200 Claw domain apo form Deposited 2020-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1490–1594（105 aa） Chain D 1490–1594（105 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium citrate tribasic dihydrate pH 5.0, Jeffamine ED-2001 pH 7.0	Resolution 1.80 Å R-free 0.230
7CZM Crystal structure of FIP200 Claw/p-OPtineurin LIR complex Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1490–1594（105 aa） Chain B 1490–1594（105 aa）	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Potassium iodide, MES pH 6.5, PEG 4000	Resolution 2.00 Å R-free 0.223
7D0E Crystal structure of FIP200 Claw/p-CCPG1 FIR2 Deposited 2020-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1490–1594（105 aa）	Not recorded	GO9 3-(2-hydroxyethyloxy)-2-[2-(2-hydroxyethyloxy)ethoxymethyl]-2-(2-hydroxyethyloxymethyl)propan-1-ol × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；KCl, Pentaerythritol ethoxylate (15/4 EO/OH), MES	Resolution 1.40 Å R-free 0.207
7EA2 crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain Deposited 2021-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1490–1594（105 aa） Chain B 1490–1594（105 aa）	Not recorded	P6G HEXAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M phosphate/citrate pH 4.2, 40% PEG300	Resolution 2.14 Å R-free 0.232
7EAA crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain Deposited 2021-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1286–1395（110 aa） Chain D 1286–1395（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M MgCl2, 0.1 M MES pH 6.0, 8% PEG6000	Resolution 2.60 Å R-free 0.253
8SOI Structure of human ULK1 complex core (2:1:1 stoichiometry) Deposited 2023-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–600（600 aa） Chain B 1–600（600 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8SQZ Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture Deposited 2023-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–640（640 aa） Chain B 1–640（640 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.85 Å
8SRM Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–640（640 aa） Chain B 1–640（640 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å
8W6B crystal structure of TAX1BP1 SKICH domain in complex with RB1CC1 coiled-coil domain Deposited 2023-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1343–1395（53 aa） Chain D 1343–1395（53 aa） Chain G 1343–1395（53 aa） Chain H 1343–1395（53 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；5% (w/v) PEG 4000, 50 mM Magnesium chloride, 100 mM MES at pH 6.5, 10% 2-propanol	Resolution 2.39 Å R-free 0.234
8YFL crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123 Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1490–1594（105 aa） Fragment：claw domain	Not recorded	GOL GLYCEROL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 6000, 0.1M MES, 5% v/v MPD, pH 6.5	Resolution 1.50 Å R-free 0.218
8YFL crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123 Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1490–1594（105 aa） Fragment：claw domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 6000, 0.1M MES, 5% v/v MPD, pH 6.5	Resolution 1.50 Å R-free 0.218
8YFM Crystal structure of FIP200 claw/TNIP1_FIR_pS122 Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1490–1594（105 aa） Fragment：claw domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；25% v/v PEG smear medium, 0.1M sodium cacodylate, 0.2M ammonium sulfate, pH 5.5	Resolution 1.50 Å R-free 0.209
8YFM Crystal structure of FIP200 claw/TNIP1_FIR_pS122 Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1490–1594（105 aa） Fragment：claw domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；25% v/v PEG smear medium, 0.1M sodium cacodylate, 0.2M ammonium sulfate, pH 5.5	Resolution 1.50 Å R-free 0.209
8YFN Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an elongated C terminus Deposited 2024-02-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1490–1594（105 aa） Fragment：claw domain	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2M imidazole malate, pH 5.5, 42% PEG 600	Resolution 2.30 Å R-free 0.236
8YFN Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an elongated C terminus Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1490–1594（105 aa） Fragment：claw domain	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2M imidazole malate, pH 5.5, 42% PEG 600	Resolution 2.30 Å R-free 0.236
9C82 Structure of human ULK1C:PI3KC3-C1 supercomplex Deposited 2024-06-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–640（640 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；added 0.05% (w/v) octylglucopyranoside as surfactant	Resolution 6.84 Å
9D34 FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1 FIP200 interacting peptide Deposited 2024-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1490–1594（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Morpheus E4 (12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each ethylene glycol, 0.1 M MES/imidazole pH 6.5)	Resolution 1.42 Å R-free 0.234
9J54 Crystal structure of FIP200 Claw in complex with ATG16L1 Deposited 2024-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1490–1594（105 aa） Chain C 1490–1594（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；10% v/v 2-Propanol, 0.1 M BICINE (pH 8.5), 30% w/v Polyethylene glycol 1500	Resolution 1.61 Å R-free 0.216

17 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBCC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 1490–1594 Author chain C； PDBConstruct 1–105； UniProt 1490–1594 Author chain E； PDBConstruct 1–105； UniProt 1490–1594 Author chain G； PDBConstruct 1–105； UniProt 1490–1594

TNIP1_FIR_pS123 peptide

OrganismNot specified

UniProt Q15025

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 118–128	Non-standard monomer：Yes (specific site not provided by mmCIF)	RB1-inducible coiled-coil protein 1 × 1 （Q8TDY2） MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 118–128	Non-standard monomer：Yes (specific site not provided by mmCIF)	RB1-inducible coiled-coil protein 1 × 1 （Q8TDY2） MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 118–128	Non-standard monomer：Yes (specific site not provided by mmCIF)	RB1-inducible coiled-coil protein 1 × 1 （Q8TDY2） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 118–128	Non-standard monomer：Yes (specific site not provided by mmCIF)	RB1-inducible coiled-coil protein 1 × 1 （Q8TDY2） MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5	Resolution 2.00 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8YFK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7EAL The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin Deposited 2021-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 405–513（109 aa） Chain C 405–513（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；255 K；0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400	Resolution 2.50 Å R-free 0.224
7EAL The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin Deposited 2021-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 405–513（109 aa） Chain F 405–513（109 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；255 K；0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400	Resolution 2.50 Å R-free 0.224
7EAO The structure of the A20-binding inhibitor of NF-kB 1 in complex with tri-ubiquitin Deposited 2021-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 415–513（99 aa） Chain C 415–513（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Potassium citrate tribasic, 20% PEG 3350	Resolution 2.90 Å R-free 0.283
7EB9 The structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin Deposited 2021-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 415–513（99 aa） Chain C 415–513（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M Sodium malonate pH 6.0, 10% PEG 3350	Resolution 3.20 Å R-free 0.264
8YFM Crystal structure of FIP200 claw/TNIP1_FIR_pS122 Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 118–128（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；25% v/v PEG smear medium, 0.1M sodium cacodylate, 0.2M ammonium sulfate, pH 5.5	Resolution 1.50 Å R-free 0.209
8YFM Crystal structure of FIP200 claw/TNIP1_FIR_pS122 Deposited 2024-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 118–128（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；25% v/v PEG smear medium, 0.1M sodium cacodylate, 0.2M ammonium sulfate, pH 5.5	Resolution 1.50 Å R-free 0.209
8YFN Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an elongated C terminus Deposited 2024-02-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 118–133（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2M imidazole malate, pH 5.5, 42% PEG 600	Resolution 2.30 Å R-free 0.236
8YFN Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an elongated C terminus Deposited 2024-02-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 118–133（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2M imidazole malate, pH 5.5, 42% PEG 600	Resolution 2.30 Å R-free 0.236
9D34 FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1 FIP200 interacting peptide Deposited 2024-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 120–132（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Morpheus E4 (12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each ethylene glycol, 0.1 M MES/imidazole pH 6.5)	Resolution 1.42 Å R-free 0.234

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNIP1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 118–128 Author chain D； PDBConstruct 1–11； UniProt 118–128 Author chain F； PDBConstruct 1–11； UniProt 118–128 Author chain H； PDBConstruct 1–11； UniProt 118–128

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8yfk
Deposition date deposition_date	2024-02-24
Structure title title	Crystal structure of FIP200 claw/TNIP1_FIR_pS123
Keywords keywords	phosphorylation, selective mitophagy, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.73 Å
Radius of gyration Rg (electron density) rg_electron	27.83 Å
Forward intensity I(0) i0	33285900.00
Molecular weight molecular_weight	47104.0 kDa
Excluded volume excluded_volume	59990 Å³
Envelope volume envelope_volume	77886 Å³
Hydration-shell volume shell_volume	24178 Å³
Envelope diameter envelope_diameter	91.2 Å
Shell Rg shell_rg	33.79 Å
Envelope Rg envelope_rg	27.34 Å
Shape Rg shape_rg	27.78 Å
Total Rg total_rg	28.70 Å
Total atoms total_atoms	3325
Residues n_residues	404
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.5 Å
Rg (real space) rg_real	28.75 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	3.3290e+07
I(0) uncertainty (real space) i0_real_error	4.9950e+05
Rg (reciprocal space) rg_reciprocal	28.75 Å
I(0) (reciprocal space) i0_reciprocal	33290000.0000
Solution quality estimate total_estimate	0.9008
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.749
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4761000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RB1-inducible coiled-coil protein 1
Molecular weight formula_weight	12040.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,C,E
Atom count atom_count	3516

SRHSEKIAIRDFQVGDLVLIILDERHDNYVLFTVSPTLYFLHSESLPALDLKPGEGASGASRRPWVLGKVMEKEYCQAKKAQNRFKVPLGTKFYRVKAVSWNKKV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TNIP1_FIR_pS123 peptide
Molecular weight formula_weight	1208.1 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H,D,F

SSGTSSEFEVV

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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8. Citations (1)

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Unit-cell length a length_a	37.812 Å
Unit-cell length b length_b	45.936 Å
Unit-cell length c length_c	72.951 Å
Unit-cell angle α angle_alpha	81.20 °
Unit-cell angle β angle_beta	89.67 °
Unit-cell angle γ angle_gamma	88.74 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	37.800 Å
R factor r_factor	0.1845
R_work r_work	0.1828
R_free r_free	0.2196

fit	/app/data/saxs_computation/yf/8yfk/8yfk.fit
pddf	/app/data/pr_computation/yf/8yfk/8yfk.pr.out
profile	/app/data/saxs_computation/yf/8yfk/8yfk.dat

Crystal structure of FIP200 claw/TNIP1_FIR_pS123

1. Protein Identity and Related Structures Protein Identity & Related Structures

RB1-inducible coiled-coil protein 1

State in the Current Structure

Other States of the Same Protein in the Database

TNIP1_FIR_pS123 peptide

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)