SAXSdb — 6ict

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

Histone-lysine N-methyltransferase setd3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Actin, cytoplasmic 1 × 1 （P60709） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Actin, cytoplasmic 1 × 1 （P60709） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Actin, cytoplasmic 1 × 1 （P60709） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Actin, cytoplasmic 1 × 1 （P60709） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SETD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–504； UniProt 1–503 Author chain B； PDBConstruct 2–504； UniProt 1–503 Author chain C； PDBConstruct 2–504； UniProt 1–503 Author chain D； PDBConstruct 2–504； UniProt 1–503

Actin, cytoplasmic 1

Homo sapiens

UniProt P60709

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase setd3 × 1 （Q86TU7） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase setd3 × 1 （Q86TU7） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase setd3 × 1 （Q86TU7） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone-lysine N-methyltransferase setd3 × 1 （Q86TU7） S-ADENOSYL-L-HOMOCYSTEINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACTB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–23； UniProt 66–88 Author chain G； PDBConstruct 1–23； UniProt 66–88 Author chain H； PDBConstruct 1–23； UniProt 66–88 Author chain I； PDBConstruct 1–23； UniProt 66–88

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	6ict
Deposition date deposition_date	2018-09-07
Structure title title	Structure of SETD3 bound to SAH and methylated actin
Keywords keywords	histidine methylatransferase, Structural Genomics, Structural Genomics Consortium, SGC, PROTEIN BINDING; PROTEIN BINDING
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.

6ict__assembly_1__model_1

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

Download this curve (.dat)

6ict__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ict__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.15 Å
Rg (electron density)	25.34 Å
Total Rg	26.13 Å
Atom count	3932
Residues	496
Excluded volume	70026 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ict__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ict__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6ict__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6ict__assembly_4__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase setd3
Molecular weight formula_weight	57824.7 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16956

GMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEKIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEELFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSFTYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAVKSAAVNREYYRQQMEEKAPLPKYE

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-Pichia pastoris shuttle vector pPpARG4

Entity 2 Entity 2 polymer

Description description	Actin, cytoplasmic 1
Molecular weight formula_weight	2881.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,H,I

TLKYPIEHGIVTNWDDMEKIWHH

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-Pichia pastoris shuttle vector pPpARG4

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 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	1114

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6ictA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	6ictA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

Domain ID domain_id	6ictB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	6ictB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

Domain ID domain_id	6ictC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	6ictC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

Domain ID domain_id	6ictD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	6ictD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

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Unit-cell length a length_a	59.976 Å
Unit-cell length b length_b	176.693 Å
Unit-cell length c length_c	125.892 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.952 Å
Low-resolution limit resolution_low	59.872 Å
R factor r_factor	0.1801
R_work r_work	0.1784
R_free r_free	0.2138

Structure of SETD3 bound to SAH and methylated actin

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

Histone-lysine N-methyltransferase setd3

State in the Current Structure

Other States of the Same Protein in the Database

Actin, cytoplasmic 1

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

6ict__assembly_1__model_1

6ict__assembly_1__model_1 | I(q)

6ict__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Structure of SETD3 bound to SAH and methylated actin

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

Histone-lysine N-methyltransferase setd3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin, cytoplasmic 1

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

6ict__assembly_1__model_1

6ict__assembly_1__model_1 | I(q)

6ict__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)