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5ix2

Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and unmodified H3 peptide

Method: X-RAY DIFFRACTION Dmax: 103.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MORC family CW-type zinc finger protein 3

Mus musculus

UniProt F7BJB9

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 7–456 Chain B； UniProt 7–456 Fragment：UNP residues 7-456 peptide from Histone H3.1 × 2 （P68433） ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；5% ethanol, 5% 2-Methyl-2,4-pentanediol (MPD), 0.1 M HEPES-Na Resolution 2.90 Å R-free 0.236

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 5IX2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IX1 Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3 peptide Deposited 2016-03-23 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 7–456（450 aa） Fragment：UNP residues 7-456
Chain B 7–456（450 aa） Fragment：UNP residues 7-456
Not recorded ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；5% ethanol, 5% 2-Methyl-2,4-pentanediol (MPD), 0.1 M HEPES-Na
Resolution 2.60 Å R-free 0.230

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

View Construct and Data Evidence
UniProt name MORC3_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–451； UniProt 7–456 Author chain B； PDBConstruct 2–451； UniProt 7–456

peptide from Histone H3.1

OrganismNot specified

UniProt P68433

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain P； UniProt 2–33 Chain Q； UniProt 2–33 Not recorded MORC family CW-type zinc finger protein 3 × 2 （F7BJB9） ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；5% ethanol, 5% 2-Methyl-2,4-pentanediol (MPD), 0.1 M HEPES-Na Resolution 2.90 Å R-free 0.236

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 5IX2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1U35 Crystal structure of the nucleosome core particle containing the histone domain of macroH2A Deposited 2004-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 0–135（136 aa）
Chain E 0–135（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；potassium chloride, manganese chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.00 Å R-free 0.260
2XL3 WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE Deposited 2010-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 2–9（8 aa） Fragment：AMINO TERMINAL TAIL, RESIDUES 2-9
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.2M K2SO4 20 % PEG 3350, pH 8.0
Resolution 2.70 Å R-free 0.235
2XL3 WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE Deposited 2010-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–9（8 aa） Fragment：AMINO TERMINAL TAIL, RESIDUES 2-9
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.2M K2SO4 20 % PEG 3350, pH 8.0
Resolution 2.70 Å R-free 0.235
5B1M The mouse nucleosome structure containing H3.1 Deposited 2015-12-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.34 Å R-free 0.259
5IX1 Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3 peptide Deposited 2016-03-23 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 2–16（15 aa）
Chain Q 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；5% ethanol, 5% 2-Methyl-2,4-pentanediol (MPD), 0.1 M HEPES-Na
Resolution 2.60 Å R-free 0.230
7OS4 Crystal structure of mouse CARM1 in complex with histone H3_13-31 K18 Deposited 2021-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 14–32（19 aa）
Chain F 14–32（19 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.2M Sodium malonate 0.1M MES pH 5.5 0.2M NaCl
Resolution 2.54 Å R-free 0.255
7OS4 Crystal structure of mouse CARM1 in complex with histone H3_13-31 K18 Deposited 2021-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 14–32（19 aa）
Chain H 14–32（19 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；1.2M Sodium malonate 0.1M MES pH 5.5 0.2M NaCl
Resolution 2.54 Å R-free 0.255

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H31_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain P； PDBConstruct 1–32； UniProt 2–33 Author chain Q； PDBConstruct 1–32； UniProt 2–33

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 5ix2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ix2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ix2
Deposition date deposition_date2016-03-23
Structure title titleCrystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and unmodified H3 peptide
Keywords keywordsMorc3, ATPase, CW domain, H3, TRANSCRIPTION; TRANSCRIPTION
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_guinier30.52 Å
Radius of gyration Rg (electron density) rg_electron29.73 Å
Forward intensity I(0) i0162144000.00
Molecular weight molecular_weight100580.0 kDa
Excluded volume excluded_volume125710 ų
Envelope volume envelope_volume155880 ų
Hydration-shell volume shell_volume42797 ų
Envelope diameter envelope_diameter110.8 Å
Shell Rg shell_rg37.54 Å
Envelope Rg envelope_rg30.02 Å
Shape Rg shape_rg29.68 Å
Total Rg total_rg30.57 Å
Total atoms total_atoms7049
Residues n_residues862
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 dmax103.7 Å
Rg (real space) rg_real30.49 Å
Rg uncertainty (real space) rg_real_error0.85 Å
I(0) (real space) i0_real1.6210e+08
I(0) uncertainty (real space) i0_real_error2.5410e+06
Rg (reciprocal space) rg_reciprocal30.50 Å
I(0) (reciprocal space) i0_reciprocal162100000.0000
Solution quality estimate total_estimate0.8706
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.9 Å
Skewness Skewness skewness0.356
Kurtosis Kurtosis kurtosis-0.210
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35690000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.898
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5ix2A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily100 —
Domain ID domain_id5ix2B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily100 —
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8. Citations (1)

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9. Files and Curves (10)