SAXSdb — 5ix1

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

MORC family CW-type zinc finger protein 3

Mus musculus

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 2.60 Å R-free 0.230

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 5IX1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5IX2 Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and unmodified H3 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 2.90 Å R-free 0.236

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 2–16 Chain Q； UniProt 2–16	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 2.60 Å R-free 0.230

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 5IX1	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 mutation/modification 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 mutation/modification 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
5IX2 Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and unmodified H3 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 2–33（32 aa） Chain Q 2–33（32 aa）	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 2.90 Å R-free 0.236
7OS4 Crystal structure of mouse CARM1 in complex with histone H3_13-31 K18 Deposited 2021-06-07	Different construct 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 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 1–15； UniProt 2–16 Author chain Q； PDBConstruct 1–15； UniProt 2–16

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	5ix1
Deposition date deposition_date	2016-03-23
Structure title title	Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3 peptide
Keywords keywords	Morc3, ATPase, CW domain, H3K4me3, TRANSCRIPTION; TRANSCRIPTION
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	30.40 Å
Radius of gyration Rg (electron density) rg_electron	29.60 Å
Forward intensity I(0) i0	158642000.00
Molecular weight molecular_weight	99522.0 kDa
Excluded volume excluded_volume	124400 Å³
Envelope volume envelope_volume	154570 Å³
Hydration-shell volume shell_volume	42616 Å³
Envelope diameter envelope_diameter	111.2 Å
Shell Rg shell_rg	37.47 Å
Envelope Rg envelope_rg	29.86 Å
Shape Rg shape_rg	29.55 Å
Total Rg total_rg	30.44 Å
Total atoms total_atoms	6975
Residues n_residues	850
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	104.2 Å
Rg (real space) rg_real	30.37 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.5860e+08
I(0) uncertainty (real space) i0_real_error	2.2540e+06
Rg (reciprocal space) rg_reciprocal	30.38 Å
I(0) (reciprocal space) i0_reciprocal	158600000.0000
Solution quality estimate total_estimate	0.8675
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.365
Kurtosis Kurtosis kurtosis	-0.190
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34020000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.912

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	MORC family CW-type zinc finger protein 3
Molecular weight formula_weight	51950.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7042

STGIRLSALCPKFLHTNSTSHTWPFSAVAELIDNAYDPDVNAKQIWIDKTVISDHICLTFTDNGNGMTADKLHKMLSFGFSDKVTMNGHVPVGLYGNGFKSGSMRLGKDAMVFTKNGETMSVGFLSQTYLEVIKAEHVVVPIVTFNKHRQMINLTESKASLAAILEHSLFSTEQKLLAELNAIMGKKGTRIIIWNLRSYKNATEFDFEKDKYDIRIPEDLDETAGRKGYKKQERMDQIAPESDYSLRAYCSILYLKPRMQIIIRGQKVKTQLVSKSLAYIERDVYRPKFLTRTVRITFGFNCRNKDHYGIMMYHKNRLIKAYEKVGCQLKANNMGVGVVGIIECNFLKPTHNKQDFDYTNEYRLTILALGEKLNDYWNEMKVKKNAEYPVNLPVEDIQKRPDQTWVQCDACLKWRKLPDGIDQLPEKWYCSNNPDPQFRNCEVPEEPEDED

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide from Histone H3.1
Molecular weight formula_weight	1607.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

ARTKQTARKSTGGKA

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	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ix1A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5ix1B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	100 —

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8. Citations (1)

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Unit-cell length a length_a	111.353 Å
Unit-cell length b length_b	149.079 Å
Unit-cell length c length_c	173.473 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.762 Å
R factor r_factor	0.2182
R_work r_work	0.2176
R_free r_free	0.2296

fit	/app/data/saxs_computation/ix/5ix1/5ix1.fit
pddf	/app/data/pr_computation/ix/5ix1/5ix1.pr.out
profile	/app/data/saxs_computation/ix/5ix1/5ix1.dat

Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3 peptide

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

MORC family CW-type zinc finger protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Peptide from Histone H3.1

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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)