4apf

Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution

Method: X-RAY DIFFRACTION D_max: 127.0 Å Quality: GOOD

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

KELCH-LIKE PROTEIN 11

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 A； UniProt 67–340	Fragment：BTB DOMAIN, BACK DOMAIN, RESIDUES 67-340	CULLIN 3 × 2 （Q13618）	X-RAY DIFFRACTION X-ray crystallization conditions：0.12 M K CITRATE; 17% PEG 3350; 10% ETHYLENE GLYCOL; PH 6.5 BIS TRIS PROPANE	Resolution 3.10 Å R-free 0.222

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 4APF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3I3N Crystal structure of the BTB-BACK domains of human KLHL11 Deposited 2009-06-30	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 67–340（274 aa） Fragment：BTB-BACK domains (UNP residues 67-340) Chain B 67–340（274 aa） Fragment：BTB-BACK domains (UNP residues 67-340)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.25M K thiocyanate, 25w/v PEG 3350, 5v/v ethylene glycol, bis tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.60 Å R-free 0.286
4AP2 Crystal structure of the human KLHL11-Cul3 complex at 2.8A resolution Deposited 2012-03-30	Different construct 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 67–340（274 aa） Fragment：BTB AND BACK DOMAIN, RESIDUES 67-340	Not recorded	EDO 1,2-ETHANEDIOL × 4 IOD IODIDE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG3350, 0.15M NAI, 8% ETHGLY	Resolution 2.80 Å R-free 0.236

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KLH11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–297； UniProt 67–340

CULLIN 3

HOMO SAPIENS

UniProt Q13618

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 B； UniProt 23–388	Fragment：N-TERMINAL DOMAIN, RESIDUES 23-388 Mutation：YES	KELCH-LIKE PROTEIN 11 × 2 （Q9NVR0）	X-RAY DIFFRACTION X-ray crystallization conditions：0.12 M K CITRATE; 17% PEG 3350; 10% ETHYLENE GLYCOL; PH 6.5 BIS TRIS PROPANE	Resolution 3.10 Å R-free 0.222

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4APF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MYL Cullin3 - BTB interface: a novel target for stapled peptides Deposited 2015-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–68（20 aa） Fragment：UNP residues 49-68	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；298 K；Pressure ambient NMR sample composition 1 mM Cul349-68EN, trifluoroethanol/water \| trifluoroethanol/water	Resolution not provided
2MYM Cullin3 - BTB interface: a novel target for stapled peptides Deposited 2015-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–68（20 aa） Fragment：UNP residues 49-68	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；298 K；Pressure ambient NMR sample composition 1 mM Cul349-68LA, trifluoroethanol/water \| trifluoroethanol/water	Resolution not provided
4AP2 Crystal structure of the human KLHL11-Cul3 complex at 2.8A resolution Deposited 2012-03-30	Different construct 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 1–388（388 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-388	Mutation：YES	EDO 1,2-ETHANEDIOL × 4 IOD IODIDE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG3350, 0.15M NAI, 8% ETHGLY	Resolution 2.80 Å R-free 0.236
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381 Chain D 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381	Mutation：I342R, L346D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I342R, L346D 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, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381	Mutation：I342R, L346D 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, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381	Mutation：I342R, L346D 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, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.263
4HXI Crystal structure of KLHL3/Cul3 complex Deposited 2012-11-10	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 B 20–381（362 aa） Fragment：NTD	Mutation：K274R, I342R, L346D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M ammonium tartrate, 14% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.51 Å R-free 0.278
5NLB Crystal structure of human CUL3 N-terminal domain bound to KEAP1 BTB and 3-box Deposited 2017-04-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 26–381（356 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG3350, 10% ethylene glycol, 0.2M potassium citrate tribasic	Resolution 3.45 Å R-free 0.288
6I2M Crystal structure of vaccinia virus protein A55 BTB-Back domain in complex with human Cullin-3 N-terminus Deposited 2018-11-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 23–388（366 aa）	Mutation：I342R and L346D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.29% tacsimate pH 6.5, 9.92% PEG3350	Resolution 2.30 Å R-free 0.282
8GQ6 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex Deposited 2022-08-29	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 C 1–768（768 aa） Chain F 1–768（768 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8H33 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex Deposited 2022-10-07	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 × 12 PDB declaration: dodecameric	Chain C 1–768（768 aa） Chain F 1–768（768 aa） Chain H 1–768（768 aa） Chain I 1–768（768 aa）	Not recorded	ZN ZINC ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.86 Å
8H34 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex Deposited 2022-10-07	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 × 18 PDB declaration: octadecameric	Chain C 1–768（768 aa） Chain F 1–768（768 aa） Chain H 1–768（768 aa） Chain I 1–768（768 aa） Chain M 1–768（768 aa） Chain O 1–768（768 aa）	Not recorded	ZN ZINC ION × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.99 Å
8H35 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex Deposited 2022-10-08	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 × 24 PDB declaration: 24-meric	Chain C 1–768（768 aa） Chain F 1–768（768 aa） Chain H 1–768（768 aa） Chain I 1–768（768 aa） Chain M 1–768（768 aa） Chain O 1–768（768 aa） Chain T 1–768（768 aa） Chain V 1–768（768 aa）	Not recorded	ZN ZINC ION × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.41 Å
8H36 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex Deposited 2022-10-08	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 × 8 PDB declaration: octameric	Chain C 1–768（768 aa） Chain F 1–768（768 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
8H37 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex Deposited 2022-10-08	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 × 16 PDB declaration: hexadecameric	Chain C 1–768（768 aa） Chain F 1–768（768 aa） Chain M 1–768（768 aa） Chain O 1–768（768 aa）	Not recorded	ZN ZINC ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.52 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08	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 × 13 PDB declaration: tridecameric	Chain L 1–768（768 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8	Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08	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 × 12 PDB declaration: dodecameric	Chain L 1–768（768 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08	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 × 12 PDB declaration: dodecameric	Chain L 1–768（768 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.73 Å
8H3Q Cryo-EM Structure of the CAND1-Cul3-Rbx1 complex Deposited 2022-10-09	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 × 3 PDB declaration: trimeric	Chain C 1–768（768 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
8H3R Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex Deposited 2022-10-09	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 C 1–768（768 aa） Chain F 1–768（768 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.36 Å
8I79 Cryo-EM structure of KCTD7 in complex with Cullin3 Deposited 2023-01-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain B 22–388（367 aa） Chain C 22–388（367 aa） Chain E 22–388（367 aa） Chain H 22–388（367 aa） Chain J 22–388（367 aa）	Mutation：I342R, L346D Mutation：I342R, L346D Mutation：I342R, L346D Mutation：I342R, L346D Mutation：I342R, L346D	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8K8T Structure of CUL3-RBX1-KLHL22 complex Deposited 2023-07-31	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–768（768 aa） Chain D 1–768（768 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8K9I Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif Deposited 2023-08-01	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 25–768（744 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8KHP CULLIN3-KLHL22-RBX1 E3 ligase Deposited 2023-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–768（768 aa） Chain D 1–768（768 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.67 Å
8U80 KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD) Deposited 2023-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain C1 1–381（381 aa） Chain C2 1–381（381 aa） Chain C3 1–381（381 aa） Chain C4 1–381（381 aa） Chain C5 1–381（381 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8U81 KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map Deposited 2023-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain C1 1–381（381 aa） Chain C2 1–381（381 aa） Chain C3 1–381（381 aa） Chain C4 1–381（381 aa） Chain C5 1–381（381 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
8U82 KCTD5/Cullin3/Gbeta1gamma2 Complex: State B From Composite RELION Multi-body Refinement Map Deposited 2023-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain C1 2–381（380 aa） Chain C2 2–381（380 aa） Chain C3 2–381（380 aa） Chain C4 2–381（380 aa） Chain C5 2–381（380 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8U83 KCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION Multi-body Refinement Map Deposited 2023-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain C1 1–381（381 aa） Fragment：UNP residues 1-381 Chain C2 1–381（381 aa） Fragment：UNP residues 1-381 Chain C3 1–381（381 aa） Fragment：UNP residues 1-381 Chain C4 1–381（381 aa） Fragment：UNP residues 1-381 Chain C5 1–381（381 aa） Fragment：UNP residues 1-381	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.98 Å
8U84 KCTD5/Cullin3/Gbeta1gamma2 Complex: State D From Composite RELION Multi-body Refinement Map Deposited 2023-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain C1 1–381（381 aa） Chain C2 1–381（381 aa） Chain C3 1–381（381 aa） Chain C4 1–381（381 aa） Chain C5 1–381（381 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21	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 × 11 PDB declaration: undecameric	Chain J 1–768（768 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9RWZ ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO Deposited 2025-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain H 1–390（390 aa） Chain I 1–390（390 aa）	Mutation：I342R, L346D Mutation：I342R, L346D	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；25 mM HEPES, 50 mM NaCl, 1 mM TCEP, pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å

29 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CUL3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–366； UniProt 23–388

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4apf
Deposition date deposition_date	2012-04-02
Structure title title	Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution
Keywords keywords	UBIQUITINATION, E3 LIGASE, CELL CYCLE; CELL CYCLE
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	37.63 Å
Radius of gyration Rg (electron density) rg_electron	37.60 Å
Forward intensity I(0) i0	67655900.00
Molecular weight molecular_weight	65702.0 kDa
Excluded volume excluded_volume	82140 Å³
Envelope volume envelope_volume	121200 Å³
Hydration-shell volume shell_volume	28779 Å³
Envelope diameter envelope_diameter	131.8 Å
Shell Rg shell_rg	40.24 Å
Envelope Rg envelope_rg	37.15 Å
Shape Rg shape_rg	37.63 Å
Total Rg total_rg	37.69 Å
Total atoms total_atoms	4626
Residues n_residues	605
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	127.0 Å
Rg (real space) rg_real	37.99 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	6.7660e+07
I(0) uncertainty (real space) i0_real_error	1.1070e+06
Rg (reciprocal space) rg_reciprocal	37.77 Å
I(0) (reciprocal space) i0_reciprocal	67640000.0000
Solution quality estimate total_estimate	0.8177
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	-0.648
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4503000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.652; Smooth: 0.643

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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	KELCH-LIKE PROTEIN 11
Molecular weight formula_weight	34526.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4641

MHHHHHHSSGVDLGTENLYFQSMEAEDFECSSHCSELSWRQNEQRRQGLFCDITLCFGGAGGREFRAHRSVLAAATEYFTPLLSGQFSESRSGRVEMRKWSSEPGPEPDTVEAVIEYMYTGRIRVSTGSVHEVLELADRFLLIRLKEFCGEFLKKKLHLSNCVAIHSLAHMYTLSQLALKAADMIRRNFHKVIQDEEFYTLPFHLIRDWLSDLEITVDSEEVLFETVLKWVQRNAEERERYFEELFKLLRLSQMKPTYLTRHVKPERLVANNEVCVKLVADAVERHALRAENIQSGT

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	CULLIN 3
Molecular weight formula_weight	45724.0 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRNAYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDRGAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYRQGLDDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLNLNSRSPEYLAENLYFQSHHHHHHDYKDDDDK

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4apfb_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.17 — Cullin repeat-like
Family Family family	a.118.17.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	4apfA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	4apfA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	420 —

Domain ID domain_id	4apfB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	4apfB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	4apfB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

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8. Citations (1)

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Unit-cell length a length_a	238.640 Å
Unit-cell length b length_b	41.440 Å
Unit-cell length c length_c	147.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	35.880 Å
R factor r_factor	0.1945
R_work r_work	0.1930
R_free r_free	0.2218

fit	/app/data/saxs_computation/ap/4apf/4apf.fit
pddf	/app/data/pr_computation/ap/4apf/4apf.pr.out
profile	/app/data/saxs_computation/ap/4apf/4apf.dat

Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution

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

KELCH-LIKE PROTEIN 11

State in the Current Structure

Other States of the Same Protein in the Database

CULLIN 3

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

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)