6luk

Crystal structure of the SAMD1 SAM domain in another crystal form

Method: X-RAY DIFFRACTION

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

Atherin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 5 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 4 water × 5	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 4 water × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 5	SULFATE ION × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAMD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–69； UniProt 459–526 Author chain B； PDBConstruct 2–69； UniProt 459–526 Author chain C； PDBConstruct 2–69； UniProt 459–526 Author chain D； PDBConstruct 2–69； UniProt 459–526 Author chain E； PDBConstruct 2–69； UniProt 459–526 Author chain F； PDBConstruct 2–69； UniProt 459–526 Author chain G； PDBConstruct 2–69； UniProt 459–526 Author chain H； PDBConstruct 2–69； UniProt 459–526 Author chain I； PDBConstruct 2–69； UniProt 459–526 Author chain J； PDBConstruct 2–69； UniProt 459–526 Author chain K； PDBConstruct 2–69； UniProt 459–526 Author chain L； PDBConstruct 2–69； UniProt 459–526 Author chain M； PDBConstruct 2–69； UniProt 459–526 Author chain N； PDBConstruct 2–69； UniProt 459–526 Author chain O； PDBConstruct 2–69； UniProt 459–526 Author chain P； PDBConstruct 2–69； UniProt 459–526 Author chain Q； PDBConstruct 2–69； UniProt 459–526 Author chain R； PDBConstruct 2–69； UniProt 459–526 Author chain S； PDBConstruct 2–69； UniProt 459–526 Author chain T； PDBConstruct 2–69； UniProt 459–526

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	6luk
Deposition date deposition_date	2020-01-29
Structure title title	Crystal structure of the SAMD1 SAM domain in another crystal form
Keywords keywords	CpG-islands, transcription, decamer, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

6luk__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6luk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6luk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.66 Å
Rg (electron density)	22.61 Å
Total Rg	23.38 Å
Atom count	2770
Residues	345
Excluded volume	49546 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6luk__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6luk__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6luk__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6luk__assembly_4__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Atherin
Molecular weight formula_weight	7810.9 kDa
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Atom count atom_count	11923

SPVEWTVMDVVEYFTEAGFPEQATAFQEQEIDGKSLLLMQRTDVLTGLSIRLGPALKIYEHHIKVLQQG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia Coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	833

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (40 domains)

Domain ID domain_id	d6luka1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6luka2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukb1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukc1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukd1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6luke1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6luke2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukf1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukg1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukg2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukh1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6luki1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6luki2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukj1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukj2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukk1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukk2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukl1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukl2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukm1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukm2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukn1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukn2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6luko1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6luko2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukp1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukp2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukq1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukq2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukr1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukr2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6luks1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6luks2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6lukt1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d6lukt2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	66.430 Å
Unit-cell length b length_b	182.842 Å
Unit-cell length c length_c	66.971 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.054 Å
Low-resolution limit resolution_low	45.710 Å
R factor r_factor	0.1872
R_work r_work	0.1852
R_free r_free	0.2259

Crystal structure of the SAMD1 SAM domain in another crystal form

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

Atherin

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

6luk__assembly_2__model_1

6luk__assembly_2__model_1 | I(q)

6luk__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (40 domains)

7. Citations (1)

Crystal structure of the SAMD1 SAM domain in another crystal form

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

Atherin

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

6luk__assembly_2__model_1

6luk__assembly_2__model_1 | I(q)

6luk__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (40 domains)

7. Citations (1)