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5j28

Ki67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex

Method: X-RAY DIFFRACTION Dmax: 87.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein phosphatase PP1-gamma catalytic subunit

Homo sapiens

UniProt P36873

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 7–308 Fragment：UNP residues 7-308 Antigen KI-67 × 1 （P46013） MLI MALONATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；1.9 M Sodium Malonate pH 4.0 Resolution 2.00 Å R-free 0.197
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 7–308 Fragment：UNP residues 7-308 Antigen KI-67 × 1 （P46013） MLI MALONATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；1.9 M Sodium Malonate pH 4.0 Resolution 2.00 Å R-free 0.197

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 5J28 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IT6 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1 Deposited 2002-01-09 Different construct 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 1–323（323 aa）
Not recorded MN MANGANESE (II) ION × 2 CYU CALYCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；PEG3350, POTASSIUM SULFATE, MANGANESE(II) CHLORIDE, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.218
1IT6 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1 Deposited 2002-01-09 Different construct 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 1–323（323 aa）
Not recorded MN MANGANESE (II) ION × 2 CYU CALYCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；PEG3350, POTASSIUM SULFATE, MANGANESE(II) CHLORIDE, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.218
1JK7 CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1 Deposited 2001-07-11 Different construct 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 1–323（323 aa）
Not recorded MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 1 OKA OKADAIC ACID × 1 BME BETA-MERCAPTOETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；LITHIUM SULPHATE, PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.225
1U32 Crystal structure of a Protein Phosphatase-1: Calcineurin Hybrid Bound to Okadaic Acid Deposited 2004-07-20 Different construct 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 6–298（293 aa） Fragment：residues 6-298
Not recorded MN MANGANESE (II) ION × 2 OKA OKADAIC ACID × 1 BME BETA-MERCAPTOETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；lithium sulfate, tris, PEG 400, mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.254
2BCD X-ray crystal structure of Protein Phosphatase-1 with the marine toxin motuporin bound Deposited 2005-10-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–323（323 aa）
Not recorded BME BETA-MERCAPTOETHANOL × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；273 K；2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%), beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 2.10 Å R-free 0.264
2BDX X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1 Deposited 2005-10-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–323（323 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；273 K；2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%) and beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 2.30 Å R-free 0.250
4UT2 X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate Deposited 2014-07-17 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 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；19.3 % PEG 3350, 200 MM NACL, 100 MM TRIS PH 9.0 SOAKING IN RESERVOIR ENRICHED BY 25MM ASCORBATE FOR 30 MINUTES CRYOPROTECTION 20% GLYCEROL
Resolution 1.96 Å R-free 0.201
4UT2 X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate Deposited 2014-07-17 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 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；19.3 % PEG 3350, 200 MM NACL, 100 MM TRIS PH 9.0 SOAKING IN RESERVOIR ENRICHED BY 25MM ASCORBATE FOR 30 MINUTES CRYOPROTECTION 20% GLYCEROL
Resolution 1.96 Å R-free 0.201
4UT3 X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide Deposited 2014-07-17 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 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD
Resolution 2.19 Å R-free 0.211
4UT3 X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide Deposited 2014-07-17 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 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD
Resolution 2.19 Å R-free 0.211
5INB RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex Deposited 2016-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 7–308（302 aa） Fragment：UNP residues 7-308
Not recorded MLI MALONATE ION × 1 GOL GLYCEROL × 6 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.3；277 K；1 M Sodium Malonate
Resolution 1.30 Å R-free 0.153
7SD0 Cryo-EM structure of the SHOC2:PP1C:MRAS complex Deposited 2021-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–323（323 aa）
Not recorded GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Used the "perpetually hydrated" method of applying graphene oxide. (Cheung et al., 2018)
Resolution 2.95 Å
8B5R p97-p37-SPI substrate complex Deposited 2022-09-24 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 P 1–323（323 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PP1G_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–305； UniProt 7–308 Author chain B； PDBConstruct 4–305； UniProt 7–308

Antigen KI-67

Homo sapiens

UniProt P46013

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 C； UniProt 496–536 Fragment：UNP residues 496-536 Mutation：T525M Serine/threonine-protein phosphatase PP1-gamma catalytic subunit × 1 （P36873） MLI MALONATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；1.9 M Sodium Malonate pH 4.0 Resolution 2.00 Å R-free 0.197
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 496–536 Fragment：UNP residues 496-536 Mutation：T525M Serine/threonine-protein phosphatase PP1-gamma catalytic subunit × 1 （P36873） MLI MALONATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；1.9 M Sodium Malonate pH 4.0 Resolution 2.00 Å R-free 0.197

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 5J28 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1R21 Solution Structure of human Ki67 FHA Domain Deposited 2003-09-25 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 1–120（120 aa） Fragment：FHA domain
Mutation：none No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8.4；290 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR measurement conditions pH 7.5；290 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure ambient
NMR sample composition 0.5 mM U-13C,15N-protein; 10 mM TrisHCl buffer (pH 8.4); 2mM DTT; 1 mM EDTA | 95% H2O, 10% D2O
NMR sample composition 0.5 mM U-13C,15N-protein; 5 mM HEPES buffer (pH 7.5); 2mM DTT; 1 mM EDTA; 150 mM NaCl | 95% H2O, 10% D2O
NMR sample composition 0.5 mM unlabeled-protein; 10 mM TrisHCl buffer (pH 8.4); 2mM DTT; 1 mM EDTA | 95% H2O, 10% D2O
NMR sample composition 0.5 mM unlabeled-protein; 10 mM TrisHCl buffer (pH 8.4); 2mM DTT; 1 mM EDTA | 100% D2O
Resolution not provided
2AFF The solution structure of the Ki67FHA/hNIFK(226-269)3P complex Deposited 2005-07-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–120（120 aa） Fragment：FHA domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；293 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure ambient
NMR sample composition 0.9 mM Ki67 FHA U-15N,13C; 1 mM hNIFK(226-269)3P unlabeled 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.4 | 93% H2O/7% D2O
NMR sample composition 0.9 mM Ki67 FHA U-15N,13C; 1 mM hNIFK(226-269)3P unlabeled 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.4 | 100% D2O
NMR sample composition 1 mM Ki67 FHA unlabled; 0.9 mM hNIFK(226-269)3P U-15N,13C 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.4 | 93% H2O/7% D2O
NMR sample composition 1 mM Ki67 FHA unlabled; 0.9 mM hNIFK(226-269)3P U-15N,13C 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.4 | 100% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name KI67_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 6–46； UniProt 496–536 Author chain D； PDBConstruct 6–46； UniProt 496–536

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

SAXS profile for 5j28

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5j28
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5j28
Deposition date deposition_date2016-03-29
Structure title titleKi67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex
Keywords keywordsPP1 gamma; RepoMan, Ki-67; Phosphatase, HYDROLASE-PROTEIN BINDING complex; HYDROLASE/PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.71 Å
Radius of gyration Rg (electron density) rg_electron27.10 Å
Forward intensity I(0) i084852300.00
Molecular weight molecular_weight73158.0 kDa
Excluded volume excluded_volume91738 ų
Envelope volume envelope_volume106980 ų
Hydration-shell volume shell_volume32537 ų
Envelope diameter envelope_diameter90.6 Å
Shell Rg shell_rg34.91 Å
Envelope Rg envelope_rg27.12 Å
Shape Rg shape_rg27.06 Å
Total Rg total_rg28.02 Å
Total atoms total_atoms5149
Residues n_residues652
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.3 Å
Rg (real space) rg_real27.71 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real8.4850e+07
I(0) uncertainty (real space) i0_real_error1.2800e+06
Rg (reciprocal space) rg_reciprocal27.71 Å
I(0) (reciprocal space) i0_reciprocal84850000.0000
Solution quality estimate total_estimate0.8988
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1 Å
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26700000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.924
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5j28a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd5j28b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id5j28A00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id5j28B00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
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8. Citations (1)

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9. Files and Curves (10)