4d0p

Crystal structure of human CSN4

Method: X-RAY DIFFRACTION D_max: 103.4 Å Quality: GOOD

▼

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

COP9 SIGNALOSOME COMPLEX SUBUNIT 4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–363	Fragment：RESIDUES 1-363	NA SODIUM ION × 2 CL CHLORIDE ION × 8 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；16 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM DTT WAS MIXED EQUALLY WITH 100 MM HEPES PH 7.5, 4.3 M NACL. CRYSTALS WERE GROWN BY VAPOR DIFFUSION	Resolution 1.60 Å R-free 0.193

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 4D0P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain L 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.	Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.	Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL	Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain L 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL	Resolution 4.08 Å R-free 0.253
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.	Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain L 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.	Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain T 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.	Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain b 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.	Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain j 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.	Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain r 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.	Resolution 5.50 Å R-free 0.282
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain D 1–406（406 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28	Different construct 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 D 1–406（406 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
6R7N Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 1–406（406 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08	Different construct 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 D 1–406（406 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 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 D 1–406（406 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 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 D 1–406（406 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
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–406（406 aa）	Not recorded	6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04	Different construct 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 D 1–406（406 aa）	Not recorded	6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20	Different construct 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 D 1–406（406 aa）	Not recorded	6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21	Different construct 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 D 1–406（406 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
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08	Different construct 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 D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain D 1–406（406 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25	Different construct 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: 12-meric	Chain D 1–406（406 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain D 1–406（406 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct 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: 13-meric	Chain D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain D 1–406（406 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain D 1–406（406 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–406（406 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

28 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSN4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–387； UniProt 1–363

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4d0p
Deposition date deposition_date	2014-04-29
Structure title title	Crystal structure of human CSN4
Keywords keywords	SIGNALING PROTEIN, PCI; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.67 Å
Radius of gyration Rg (electron density) rg_electron	29.87 Å
Forward intensity I(0) i0	29916700.00
Molecular weight molecular_weight	42307.0 kDa
Excluded volume excluded_volume	52875 Å³
Envelope volume envelope_volume	69827 Å³
Hydration-shell volume shell_volume	21787 Å³
Envelope diameter envelope_diameter	104.9 Å
Shell Rg shell_rg	33.30 Å
Envelope Rg envelope_rg	30.26 Å
Shape Rg shape_rg	29.88 Å
Total Rg total_rg	30.19 Å
Total atoms total_atoms	5917
Residues n_residues	371
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

▼

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

Maximum dimension Dmax dmax	103.4 Å
Rg (real space) rg_real	30.07 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	2.9920e+07
I(0) uncertainty (real space) i0_real_error	5.3820e+05
Rg (reciprocal space) rg_reciprocal	29.90 Å
I(0) (reciprocal space) i0_reciprocal	29910000.0000
Solution quality estimate total_estimate	0.7725
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.578
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5286000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.603; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.406; Smooth: 0.829

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	COP9 SIGNALOSOME COMPLEX SUBUNIT 4
Molecular weight formula_weight	44187.1 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	6356

MASWSHPQFEKVDEENLYFQGGGRMAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLVISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFET

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	TRICHOPLUSIA NI

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4d0pA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	56.660 Å
Unit-cell length b length_b	63.530 Å
Unit-cell length c length_c	75.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	31.760 Å
R factor r_factor	0.1796
R_work r_work	0.1789
R_free r_free	0.1929

fit	/app/data/saxs_computation/d0/4d0p/4d0p.fit
pddf	/app/data/pr_computation/d0/4d0p/4d0p.pr.out
profile	/app/data/saxs_computation/d0/4d0p/4d0p.dat