SAXSdb — 6oit

▼

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

Protein RDM1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein DEFECTIVE IN MERISTEM SILENCING 3 × 4 （Q94A79） Protein CHROMATIN REMODELING 35 × 1 （Q9SIW2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RDM1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–175； UniProt 3–163 Author chain B； PDBConstruct 15–175； UniProt 3–163

Protein DEFECTIVE IN MERISTEM SILENCING 3

Arabidopsis thaliana

UniProt Q94A79

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein RDM1 × 2 （Q9LUJ3） Protein CHROMATIN REMODELING 35 × 1 （Q9SIW2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DMS3_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–423； UniProt 2–420 Author chain D； PDBConstruct 5–423； UniProt 2–420 Author chain E； PDBConstruct 5–423； UniProt 2–420 Author chain F； PDBConstruct 5–423； UniProt 2–420

Protein CHROMATIN REMODELING 35

Arabidopsis thaliana

UniProt Q9SIW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein RDM1 × 2 （Q9LUJ3） Protein DEFECTIVE IN MERISTEM SILENCING 3 × 4 （Q94A79）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHR35_ARATH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 4–58； UniProt 45–99

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6oit
Deposition date deposition_date	2019-04-09
Structure title title	CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)
Keywords keywords	SMC-hinge, Coiled-coil, SNF2, RNA-directed DNA methylation, PLANT PROTEIN; PLANT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6oit__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6oit__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6oit__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.75 Å
Rg (electron density)	39.01 Å
Total Rg	39.52 Å
Atom count	12085
Residues	1536
Excluded volume	215810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6oit__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein RDM1
Molecular weight formula_weight	20072.4 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	12085

MGSSHHHHHHSQDPSSMTMELRPSGDSGSSDVDAEISDGFSPLDTSHRDVADEGSLLRRAEMYQDYMKQVPIPTNRGSLIPFTSWVGLSISMKQLYGQPLHYLTNVLLQRWDQSRFGTDSEEQRLDSIIHPTKAEATIWLVEEIHRLTPSHLHMALLWRSDPMYHSFIDPIFPEK

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Protein DEFECTIVE IN MERISTEM SILENCING 3
Molecular weight formula_weight	49821.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F

MADLYPTGQQISFQTTPLNVQDPTRMMNLDQSSPVARNETQNGGGIAHAEFAMFNSKRLESDLEAMGNKIKQHEDNLKFLKSQKNKMDEAIVDLQVHMSKLNSSPTPRSENSDNSLQGEDINAQILRHENSAAGVLSLVETLHGAQASQLMLTKGVVGVVAKLGKVNDENLSQILSNYLGTRSMLAVVCRNYESVTALEAYDNHGNIDINAGLHCLGSSIGREIGDSFDAICLENLRPYVGQHIADDLQRRLDLLKPKLPNGECPPGFLGFAVNMIQIDPAYLLCVTSYGYGLRETLFYNLFSRLQVYKTRADMISALPCISDGAVSLDGGIIRKTGIFNLGNRDEVNVRFAKPTASRTMDNYSEAEKKMKELKWKKEKTLEDIKREQVLREHAVFNFGKKKEEFVRCLAQSSCTNQPMNTPRGTLESGKETAAAKFERQHMDSSTSAA

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Protein CHROMATIN REMODELING 35
Molecular weight formula_weight	7915.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GEFFAVSNMLEALDSGKFGSVSKELEEIADMRMDLVKRSIWLYPSLAYTVFEAEKTMDGGGGSDYKDDDDK

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21(DE3)

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6oitA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	690 — RDM1 protein domain

Domain ID domain_id	6oitB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	690 — RDM1 protein domain

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	620248

CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)

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

Protein RDM1

State in the Current Structure

Other States of the Same Protein in the Database

Protein DEFECTIVE IN MERISTEM SILENCING 3

State in the Current Structure

Other States of the Same Protein in the Database

Protein CHROMATIN REMODELING 35

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6oit__assembly_1__model_1

6oit__assembly_1__model_1 | I(q)

6oit__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

CryoEM structure of Arabidopsis DDR' complex (DRD1 peptide-DMS3-RDM1)

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

Protein RDM1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein DEFECTIVE IN MERISTEM SILENCING 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein CHROMATIN REMODELING 35

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6oit__assembly_1__model_1

6oit__assembly_1__model_1 | I(q)

6oit__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)