9f5w

Human condensin II - M18BP1 complex

Method: ELECTRON MICROSCOPY Dmax: 213.4 Å Quality: GOOD

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

Structural maintenance of chromosomes protein 2

Homo sapiens

UniProt O95347

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–1197 Not recorded Structural maintenance of chromosomes protein 4 × 1 (Q9NTJ3) Condensin-2 complex subunit D3 × 1 (P42695) Condensin-2 complex subunit H2 × 1 (Q6IBW4) Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1 × 1 (P0AEX9,Q6P0N0) Condensin-2 complex subunit G2 × 1 (Q86XI2) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMC2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1197; UniProt 1–1197

Structural maintenance of chromosomes protein 4

Homo sapiens

UniProt Q9NTJ3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–1288 Not recorded Structural maintenance of chromosomes protein 2 × 1 (O95347) Condensin-2 complex subunit D3 × 1 (P42695) Condensin-2 complex subunit H2 × 1 (Q6IBW4) Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1 × 1 (P0AEX9,Q6P0N0) Condensin-2 complex subunit G2 × 1 (Q86XI2) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMC4_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 19–1305; UniProt 2–1288

Condensin-2 complex subunit D3

Homo sapiens

UniProt P42695

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–1498 Not recorded Structural maintenance of chromosomes protein 2 × 1 (O95347) Structural maintenance of chromosomes protein 4 × 1 (Q9NTJ3) Condensin-2 complex subunit H2 × 1 (Q6IBW4) Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1 × 1 (P0AEX9,Q6P0N0) Condensin-2 complex subunit G2 × 1 (Q86XI2) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name CNDD3_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–1498; UniProt 1–1498

Condensin-2 complex subunit H2

Homo sapiens

UniProt Q6IBW4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain H; UniProt 1–605 Not recorded Structural maintenance of chromosomes protein 2 × 1 (O95347) Structural maintenance of chromosomes protein 4 × 1 (Q9NTJ3) Condensin-2 complex subunit D3 × 1 (P42695) Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1 × 1 (P0AEX9,Q6P0N0) Condensin-2 complex subunit G2 × 1 (Q86XI2) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name CNDH2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain H; PDBConstruct 1–605; UniProt 1–605

Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1

Homo sapiens

UniProt P0AEX9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain M; UniProt 26–396 Not recorded Structural maintenance of chromosomes protein 2 × 1 (O95347) Structural maintenance of chromosomes protein 4 × 1 (Q9NTJ3) Condensin-2 complex subunit D3 × 1 (P42695) Condensin-2 complex subunit H2 × 1 (Q6IBW4) Condensin-2 complex subunit G2 × 1 (Q86XI2) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

366 other PDB entries and 491 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MALE_ECOLI
Isoform
PDB entities 5
Chains and sequence ranges Author chain M; PDBConstruct 2–372; UniProt 26–396

Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1

Homo sapiens

UniProt Q6P0N0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain M; UniProt 873–1132 Not recorded Structural maintenance of chromosomes protein 2 × 1 (O95347) Structural maintenance of chromosomes protein 4 × 1 (Q9NTJ3) Condensin-2 complex subunit D3 × 1 (P42695) Condensin-2 complex subunit H2 × 1 (Q6IBW4) Condensin-2 complex subunit G2 × 1 (Q86XI2) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name M18BP_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain M; PDBConstruct 383–642; UniProt 873–1132

Condensin-2 complex subunit G2

Homo sapiens

UniProt Q86XI2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–1143 Not recorded Structural maintenance of chromosomes protein 2 × 1 (O95347) Structural maintenance of chromosomes protein 4 × 1 (Q9NTJ3) Condensin-2 complex subunit D3 × 1 (P42695) Condensin-2 complex subunit H2 × 1 (Q6IBW4) Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1 × 1 (P0AEX9,Q6P0N0) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 7.50 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name CNDG2_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain G; PDBConstruct 1–1143; UniProt 1–1143

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 9f5w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9f5w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9f5w
Deposition date deposition_date2024-04-30
Structure title titleHuman condensin II - M18BP1 complex
Keywords keywordsChromosome organisation complex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier62.24
Radius of gyration Rg (electron density) rg_electron61.93
Forward intensity I(0) i01448280000.00
Molecular weight molecular_weight327590.0 kDa
Excluded volume excluded_volume413950 ų
Envelope volume envelope_volume671520 ų
Hydration-shell volume shell_volume94903 ų
Envelope diameter envelope_diameter208.9
Shell Rg shell_rg59.54
Envelope Rg envelope_rg59.50
Shape Rg shape_rg61.95
Total Rg total_rg61.77
Total atoms total_atoms23030
Residues n_residues2849
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax213.4
Rg (real space) rg_real62.13
Rg uncertainty (real space) rg_real_error1.85
I(0) (real space) i0_real1.4480e+09
I(0) uncertainty (real space) i0_real_error2.9400e+07
Rg (reciprocal space) rg_reciprocal62.30
I(0) (reciprocal space) i0_reciprocal1449000000.0000
Solution quality estimate total_estimate0.8891
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary76.8
Skewness Skewness skewness0.155
Kurtosis Kurtosis kurtosis-0.599
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha72860000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.860

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)