SAXSdb — 7eaa

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1286–1395 Chain D； UniProt 1286–1395	Not recorded	Calcium-binding and coiled-coil domain-containing protein 2 × 2 （Q13137）	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

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 7EAA	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 mutation/modification 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 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
8SOI Structure of human ULK1 complex core (2:1:1 stoichiometry) Deposited 2023-04-28	Different construct 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 oligomeric state 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 oligomeric state 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 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
8YFK Crystal structure of FIP200 claw/TNIP1_FIR_pS123 Deposited 2024-02-24	Different construct Different mutation/modification Different oligomeric state 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	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
8YFK Crystal structure of FIP200 claw/TNIP1_FIR_pS123 Deposited 2024-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1490–1594（105 aa） Fragment：claw domain	Not recorded	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
8YFK Crystal structure of FIP200 claw/TNIP1_FIR_pS123 Deposited 2024-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1490–1594（105 aa） Fragment：claw domain	Not recorded	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
8YFK Crystal structure of FIP200 claw/TNIP1_FIR_pS123 Deposited 2024-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1490–1594（105 aa） Fragment：claw domain	Not recorded	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
8YFL crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123 Deposited 2024-02-24	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 26 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 C； PDBConstruct 5–114； UniProt 1286–1395 Author chain D； PDBConstruct 5–114； UniProt 1286–1395

Calcium-binding and coiled-coil domain-containing protein 2

Homo sapiens

UniProt Q13137

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 10–141 Chain B； UniProt 10–141	Not recorded	RB1-inducible coiled-coil protein 1 × 2 （Q8TDY2）	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

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 7EAA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MXP Solution structure of NDP52 ubiquitin-binding zinc finger Deposited 2015-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 414–446（33 aa） Fragment：C-terminal, UNP residues 414-446	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 1 mM [U-100% 15N] entity_1-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-3, 100% D2O \| 100% D2O NMR sample composition 1.2 mM entity_1-4, 100% D2O \| 100% D2O	Resolution not provided
3VVV Skich domain of NDP52 Deposited 2012-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–141（121 aa） Fragment：UNP residues 21-141	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；24% PEG4000, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.35 Å R-free 0.189
3VVV Skich domain of NDP52 Deposited 2012-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–141（121 aa） Fragment：UNP residues 21-141	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；24% PEG4000, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.35 Å R-free 0.189
3VVW NDP52 in complex with LC3C Deposited 2012-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–141（121 aa） Fragment：UNP residues 21-141	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；16% PEG6000, 0.01M sodium citrate , pH 7.0, Vapor Diffusion, temperature 293K	Resolution 2.50 Å R-free 0.252
4GXL The crystal structure of Galectin-8 C-CRD in complex with NDP52 Deposited 2012-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 368–381（14 aa） Fragment：UNP residues 368-381	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；2% PEG 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.02 Å R-free 0.216
4HAN Crystal structure of Galectin 8 with NDP52 peptide Deposited 2012-09-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 372–385（14 aa） Fragment：UNP residues 372-385 Chain D 372–385（14 aa） Fragment：UNP residues 372-385	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M Tris-Hcl pH8.5, 30~34% (v/w) PEG400, 200mM LiSO4, and 10mM Nicotinamide adenine dinucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.55 Å R-free 0.214
4XKL Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin Deposited 2015-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 414–446（33 aa） Fragment：Zinc finger, UNP residues 414-446	Not recorded	GOL GLYCEROL × 1 ACT ACETATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.243
4XKL Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin Deposited 2015-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 414–446（33 aa） Fragment：Zinc finger, UNP residues 414-446	Not recorded	GOL GLYCEROL × 1 ACT ACETATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.243
5AAQ TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy Deposited 2015-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 388–446（59 aa） Fragment：UNP RESIDUES 388-446	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0 NMR sample composition 95% WATER/5% D2O	Resolution not provided
5Z7A Crystal structure of NDP52 SKICH region Deposited 2018-01-27	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 1–126（126 aa） Fragment：UNP residues 1-126	Not recorded	SO4 SULFATE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；289 K；PEG 3350, 0.2 M potassium sulfate	Resolution 2.38 Å R-free 0.263
5Z7A Crystal structure of NDP52 SKICH region Deposited 2018-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–126（126 aa） Fragment：UNP residues 1-126	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；289 K；PEG 3350, 0.2 M potassium sulfate	Resolution 2.38 Å R-free 0.263
5Z7L Crystal structure of NDP52 SKICH region in complex with NAP1 Deposited 2018-01-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 10–126（117 aa） Fragment：UNP residues 10-126 Chain B 10–126（117 aa） Fragment：UNP residues 10-126	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG3350,sodium malonate	Resolution 2.02 Å R-free 0.222

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CACO2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 5–136； UniProt 10–141 Author chain B； PDBConstruct 5–136； UniProt 10–141

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	7eaa
Deposition date deposition_date	2021-03-06
Structure title title	crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain
Keywords keywords	NDP52 SKICH, complex, RB1CC1 coiled-coil, 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	41.19 Å
Radius of gyration Rg (electron density) rg_electron	42.84 Å
Forward intensity I(0) i0	43695800.00
Molecular weight molecular_weight	52339.0 kDa
Excluded volume excluded_volume	65409 Å³
Envelope volume envelope_volume	91950 Å³
Hydration-shell volume shell_volume	22396 Å³
Envelope diameter envelope_diameter	165.7 Å
Shell Rg shell_rg	37.91 Å
Envelope Rg envelope_rg	43.02 Å
Shape Rg shape_rg	42.78 Å
Total Rg total_rg	42.68 Å
Total atoms total_atoms	3690
Residues n_residues	441
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	161.2 Å
Rg (real space) rg_real	42.42 Å
Rg uncertainty (real space) rg_real_error	2.82 Å
I(0) (real space) i0_real	4.3700e+07
I(0) uncertainty (real space) i0_real_error	9.0460e+05
Rg (reciprocal space) rg_reciprocal	41.20 Å
I(0) (reciprocal space) i0_reciprocal	43640000.0000
Solution quality estimate total_estimate	0.6226
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.845
Kurtosis Kurtosis kurtosis	-0.201
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2369000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.055; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.015; Smooth: 0.909

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RB1-inducible coiled-coil protein 1
Molecular weight formula_weight	13565.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D
Atom count atom_count	3757

GSEFSLVAELQEKLQEEKAKFLEQLEEQEKRKNEEMQNVRTSLIAEQQTNFNTVLTREKMRKENIINDLSDKLKSTMQQQERDKDLIESLSEDRARLLEEKKKLEEEVSKLRSS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Calcium-binding and coiled-coil domain-containing protein 2
Molecular weight formula_weight	15968.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A

GPGSTSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFRPENEEDILVVTTQGE

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 BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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8. Citations (1)

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Unit-cell length a length_a	69.439 Å
Unit-cell length b length_b	69.439 Å
Unit-cell length c length_c	246.095 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	46.050 Å
R factor r_factor	0.2017
R_work r_work	0.1990
R_free r_free	0.2534

fit	/app/data/saxs_computation/ea/7eaa/7eaa.fit
pddf	/app/data/pr_computation/ea/7eaa/7eaa.pr.out
profile	/app/data/saxs_computation/ea/7eaa/7eaa.dat

crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain

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

Calcium-binding and coiled-coil domain-containing protein 2

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)