← Back to search
9qwz

Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (BP focused refinement)

Method: ELECTRON MICROSCOPY Dmax: 174.8 Å Quality: GOOD
▼

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

E3 ubiquitin-protein ligase KCMF1

Homo sapiens

UniProt Q9P0J7

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 D； UniProt 1–381 Not recorded E3 ubiquitin-protein ligase UBR4 × 1 （Q5T4S7） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.80 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.

Other PDB Difference from Current Entry 9QWZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9D9Z Structure of human UBR4-KCMF1-CaM E3 ligase complex (Silencing Factor of the Integrated stress response, SiFI) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–381（381 aa）
Chain F 1–381（381 aa）
Not recorded ZN ZINC ION × 20 CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HXW Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composite map) Deposited 2025-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–331（331 aa）
Chain D 1–331（331 aa）
Not recorded ZN ZINC ION × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9JNI KCMF1 Zn-coordinating domains with RCKG peptide (Sulfonic Cysteine) Deposited 2024-09-23 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 2–55（54 aa）
Chain A 77–142（66 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES, pH 7.0 1 M Magnesium chloride hexahydrate 20 % w/v PEG 6000 10 % v/v Ethylene glycol
Resolution 1.92 Å R-free 0.229
9NWE E3 ligase UBR4-KCMF1-calmodulin complex Deposited 2025-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–381（381 aa）
Chain F 1–381（381 aa）
Not recorded ZN ZINC ION × 6 CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9QWS Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term dimer interface focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–381（381 aa）
Chain D 1–381（381 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9QWU Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (CALM1 focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–381（381 aa）
Chain D 1–381（381 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9QX0 Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–381（381 aa）
Chain D 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 3.40 Å
9UPZ KCMF1 Zn-coordinating domains with RTGG peptide Deposited 2025-04-29 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 2–55（54 aa）
Chain A 77–136（60 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.3 M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate, 12.5% MPD, 12.5% PEG1000, 12.5% PEG 3350
Resolution 1.71 Å R-free 0.236

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCMF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain D； PDBConstruct 1–381； UniProt 1–381

E3 ubiquitin-protein ligase UBR4

Homo sapiens

UniProt Q5T4S7

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 B； UniProt 1–5183 Not recorded E3 ubiquitin-protein ligase KCMF1 × 1 （Q9P0J7） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.80 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.

Other PDB Difference from Current Entry 9QWZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8J9Q Crystal structure of UBR box of UBR4 apo Deposited 2023-05-04 Different construct 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 1660–1729（70 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)
Resolution 2.18 Å R-free 0.269
8J9Q Crystal structure of UBR box of UBR4 apo Deposited 2023-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1660–1729（70 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)
Resolution 2.18 Å R-free 0.269
8J9Q Crystal structure of UBR box of UBR4 apo Deposited 2023-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1660–1729（70 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M DL-malic acid (pH7.0) and 18% (w/v) polyethylene glycol 3350 (PEG3350)
Resolution 2.18 Å R-free 0.269
8J9R Crystal structure of UBR box of YIFS-UBR4 Deposited 2023-05-04 Different construct 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 1660–1729（70 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Bis-Tris (pH5.6), 29% (w/v) polyethylene glycol 3350 (PEG3350), 0.2 M lithium sulfate monohydrate
Resolution 1.65 Å R-free 0.287
9D9Z Structure of human UBR4-KCMF1-CaM E3 ligase complex (Silencing Factor of the Integrated stress response, SiFI) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–5183（5182 aa）
Chain B 2–5183（5182 aa）
Not recorded ZN ZINC ION × 20 CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HXW Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composite map) Deposited 2025-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–4781（4781 aa）
Chain B 1–4781（4781 aa）
Not recorded ZN ZINC ION × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9NWD Human E3 ligase UBR4-KCMF1-calmodulin complex (N-terminal) Deposited 2025-03-22 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–5183（5183 aa）
Chain B 1–5183（5183 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9NWE E3 ligase UBR4-KCMF1-calmodulin complex Deposited 2025-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–5183（5182 aa）
Chain B 2–5183（5182 aa）
Not recorded ZN ZINC ION × 6 CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9QWS Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term dimer interface focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–5183（5183 aa）
Chain B 1–5183（5183 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9QWU Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (CALM1 focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–5183（5183 aa）
Chain B 1–5183（5183 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9QWX Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (N-term focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–5183（5183 aa）
Chain B 1–5183（5183 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
9QX0 Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term focused refinement) Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–5183（5183 aa）
Chain B 1–5183（5183 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

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

View Construct and Data Evidence
UniProt name UBR4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–5183； UniProt 1–5183

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 9qwz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qwz
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9qwz
Deposition date deposition_date2025-04-15
Structure title titleCryo-EM structure of the human UBR4/KCMF1/CALM1 complex (BP focused refinement)
Keywords keywordsUbiquitin ligase, protein quality control, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier49.72 Å
Radius of gyration Rg (electron density) rg_electron50.27 Å
Forward intensity I(0) i0218875000.00
Molecular weight molecular_weight99557.0 kDa
Excluded volume excluded_volume114840 ų
Envelope volume envelope_volume266190 ų
Hydration-shell volume shell_volume46682 ų
Envelope diameter envelope_diameter172.4 Å
Shell Rg shell_rg50.92 Å
Envelope Rg envelope_rg47.83 Å
Shape Rg shape_rg50.26 Å
Total Rg total_rg50.34 Å
Total atoms total_atoms7115
Residues n_residues1433
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
▼

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

Maximum dimension Dmax dmax174.8 Å
Rg (real space) rg_real50.18 Å
Rg uncertainty (real space) rg_real_error2.15 Å
I(0) (real space) i0_real2.1890e+08
I(0) uncertainty (real space) i0_real_error4.7470e+06
Rg (reciprocal space) rg_reciprocal49.72 Å
I(0) (reciprocal space) i0_reciprocal218700000.0000
Solution quality estimate total_estimate0.8483
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.6 Å
Skewness Skewness skewness0.403
Kurtosis Kurtosis kurtosis-0.515
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14850000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.804; Smooth: 0.728
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)