SAXSdb — 9jni

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

E3 ubiquitin-protein ligase KCMF1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–55 Chain A； UniProt 77–142	Not recorded	ARG-OCS-LYS-GLY × 1 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

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 9JNI	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 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 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 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 1–331（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
9NWE E3 ligase UBR4-KCMF1-calmodulin complex Deposited 2025-03-22	Different construct 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 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 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 1–381（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 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 1–381（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
9QWZ Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (BP focused refinement) Deposited 2025-04-15	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 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 4.80 Å
9QX0 Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term focused refinement) Deposited 2025-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 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 A； PDBConstruct 1–54； UniProt 2–55 Author chain A； PDBConstruct 59–124； UniProt 77–142

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9jni
Deposition date deposition_date	2024-09-23
Structure title title	KCMF1 Zn-coordinating domains with RCKG peptide (Sulfonic Cysteine)
Keywords keywords	Complex, ZZ-domain, C2H2 Zn-finger domain, KCMF1, Arg/N-degon pathway, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	17.30 Å
Radius of gyration Rg (electron density) rg_electron	16.91 Å
Forward intensity I(0) i0	4672730.00
Molecular weight molecular_weight	13775.0 kDa
Excluded volume excluded_volume	16373 Å³
Envelope volume envelope_volume	19914 Å³
Hydration-shell volume shell_volume	11020 Å³
Envelope diameter envelope_diameter	59.5 Å
Shell Rg shell_rg	20.94 Å
Envelope Rg envelope_rg	17.00 Å
Shape Rg shape_rg	16.89 Å
Total Rg total_rg	17.64 Å
Total atoms total_atoms	1797
Residues n_residues	123
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	60.8 Å
Rg (real space) rg_real	17.45 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	4.6730e+06
I(0) uncertainty (real space) i0_real_error	5.4370e+04
Rg (reciprocal space) rg_reciprocal	17.43 Å
I(0) (reciprocal space) i0_reciprocal	4673000.0000
Solution quality estimate total_estimate	0.8046
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.0 Å
Skewness Skewness skewness	0.503
Kurtosis Kurtosis kurtosis	-0.398
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1161000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.617; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.618; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase KCMF1
Molecular weight formula_weight	13539.1 kDa
EC 编号 ec_number	2.3.2.27
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	1830

SRHEGVSCDACLKGNFRGRRYKCLICYDYDLCASCYESGATTTRHTTDHPMQCIGGGGSFTCPYCGKMGYTETSLQEHVTSEHAETSTEVICPICAALPGGDPNHVTDDFAAHLTLEHRAPRDL

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	ARG-OCS-LYS-GLY
Molecular weight formula_weight	512.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RCKG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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8. Citations (1)

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Unit-cell length a length_a	97.592 Å
Unit-cell length b length_b	97.592 Å
Unit-cell length c length_c	97.592 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 43 3 2
Space-group number int_tables_number	212
Crystal system crystal_system	cubic

Resolution resolution	1.920 Å
Low-resolution limit resolution_low	29.430 Å
R factor r_factor	0.2005
R_work r_work	0.1974
R_free r_free	0.2293

fit	/app/data/saxs_computation/jn/9jni/9jni.fit
pddf	/app/data/pr_computation/jn/9jni/9jni.pr.out
profile	/app/data/saxs_computation/jn/9jni/9jni.dat

KCMF1 Zn-coordinating domains with RCKG peptide (Sulfonic Cysteine)

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

E3 ubiquitin-protein ligase KCMF1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)