SAXSdb — 6bx3

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

Histone-lysine N-methyltransferase, H3 lysine-4 specific

Saccharomyces cerevisiae (strain YJM789)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） COMPASS component SWD1 × 1 （P39706） COMPASS component SWD3 × 1 （P38123）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6ZT27_YEAS7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–278； UniProt 799–1076

COMPASS component BRE2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P43132

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （A6ZT27） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） COMPASS component SWD1 × 1 （P39706） COMPASS component SWD3 × 1 （P38123）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRE2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain K； PDBConstruct 1–417； UniProt 87–503

COMPASS component SDC1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q03323

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （A6ZT27） COMPASS component BRE2 × 1 （P43132） COMPASS component SPP1 × 1 （Q03012） COMPASS component SWD1 × 1 （P39706） COMPASS component SWD3 × 1 （P38123）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDC1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–42； UniProt 122–163 Author chain N； PDBConstruct 1–42； UniProt 122–163

COMPASS component SPP1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q03012

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （A6ZT27） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SWD1 × 1 （P39706） COMPASS component SWD3 × 1 （P38123）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPP1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–237； UniProt 117–353

COMPASS component SWD1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P39706

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （A6ZT27） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） COMPASS component SWD3 × 1 （P38123）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SWD1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–412； UniProt 2–413

COMPASS component SWD3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38123

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （A6ZT27） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） COMPASS component SWD1 × 1 （P39706）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SWD3_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 2–315

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	6bx3
Deposition date deposition_date	2017-12-16
Structure title title	Structure of histone H3k4 methyltransferase
Keywords keywords	Histone H3K4 Methyltransferase, GENE REGULATION-Transferase complex; GENE REGULATION/Transferase
Experimental Method method	ELECTRON MICROSCOPY

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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.

6bx3__assembly_1__model_1

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

Download this curve (.dat)

6bx3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bx3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.14 Å
Rg (electron density)	45.64 Å
Total Rg	45.61 Å
Atom count	10456
Residues	1413
Excluded volume	184140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bx3__assembly_1__model_1`	heptameric （7）	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 (6)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-4 specific
Molecular weight formula_weight	32162.4 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	10456

KIWQSRRKTLEEEKASDWQIELNGTLFDSELQPGSSFKAEGFRKVTDKLKINYLPHRRRVHQPLNTVNIHNERNEYTPELCQREESSNKEPSDSVPQEVSSSRDNRASNRRFQQDIEAQKAAIGTESELLSLNQLNKRKKPVMFARSAIHNWGLYALDSIAAKEMIIEYVGERIRQPVAEMREKRYLKNGIGSSYLFRVDENTVIDATKKGGIARFINHCCDPNCTAKIIKVGGRRRIVIYALRDIAASEELTYDYKFEREKDDEERLPCLCGAPNCK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain YJM789)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	307796
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	COMPASS component BRE2
Molecular weight formula_weight	48306.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

FDHSGMSVMDRSEGLSISRDGNDLVSVPDQYGWRTARSDVCIKEGMTYWEVEVIRGGNKKFADGVNNKENADDSVDEVQSGIYEKMHKQVNDTPHLRFGVCRREASLEAPVGFDVYGYGIRDISLESIHEGKLNCVLENGSPLKEGDKIGFLLSLPSIHTQIKQAKEFTKRRIFALNSHMDTMNEPWREDAENGPSRKKLKQETTNKEFQRALLEDIEYNDVVRDQIAIRYKNQLFFEATDYVKTTKPEYYSSDKRERQDYYQLEDSYLAIFQNGKYLGKAFENLKPLLPPFSELQYNEKFYLGYWQHGEARDESNDKNTTSAKKKKQQQKKKKGLILRNKYVNNNKLGYYPTISCFNGGTARIISEEDKLEYLDQIRSAYCVDGNSKVNTLDTLYKEQIAEDIVWDIIDELEQIAL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	COMPASS component SDC1
Molecular weight formula_weight	4810.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

TRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	COMPASS component SPP1
Molecular weight formula_weight	28189.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

HGREFVNDIWSRLKTDEDRAVVKKMVEQTGHIDKFKKFGQLDFIDNNIVVKTDDEKEIFDQIVVRDMTLKTLEDDLQEVQEISLPLFKKKLELLEVYLGWLDNVYTEMRKLDDDAASHVECGKEDSKGTKRKKKKNSSRSRARKNICGYCSTYERIPCSVEEFVRDFGSNEEATKIHEVCTKWKCNRHLDWVSTNQEQYLQQIDSLESMQERLQHLIQARKKQLNIQYYEEILRRGL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 5 Entity 5 polymer

Description description	COMPASS component SWD1
Molecular weight formula_weight	47047.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NILLQDPFAVLKEHPEKLTHTIENPLRTECLQFSPCGDYLALGCANGALVIYDMDTFRPICVPGNMLGAHVRPITSIAWSPDGRLLLTSSRDWSIKLWDLSKPSKPLKEIRFDSPIWGCQWLDAKRRLCVATIFEESDAYVIDFSNDPVASLLSKSDEKQLSSTPDHGYVLVCTVHTKHPNIIIVGTSKGWLDFYKFHSLYQTECIHSLKITSSNIKHLIVSQNGERLAINCSDRTIRQYEISIDDENSAVELTLEHKYQDVINKLQWNCILFSNNTAEYLVASTHGSSAHELYIWETTSGTLVRVLEGAEEELIDINWDFYSMSIVSNGFESGNVYVWSVVIPPKWSALAPDFEEVEENVDYLEKEDEFDEVDEAEQQQGLEQEEEIAIDLRTREQYDVRGNNLLVERFTI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 6 Entity 6 polymer

Description description	COMPASS component SWD3
Molecular weight formula_weight	34655.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

FQFVTPVGTQNGLKATCAKISPDGQFLAITQGLNILIYDINRRTVSQTLVTSHARPFSELCWSPDGQCIATASDDFSVEIIHLSYGLLHTFIGHTAPVISLTFNRKGNLLFTSSMDESIKIWDTLNGSLMKTISAHSEAVVSVDVPMNDSSILSSGSYDGLIRIFDAETGHCLKTLTYDKDWKRENGVVPISQVKFSENARYLLVKSLDGVVKIWDCIGGCVVRTFQVQPLEKGVLHHSCGMDFLNPEDGSTPLVISGYENGDIYCWNSDTKSLLQLLDGSLYHHSSPVMSIHCFGNIMCSLALNGDCCLWRWV

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

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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	—

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

Resolution resolution	4.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	163539

Structure of histone H3k4 methyltransferase

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

Histone-lysine N-methyltransferase, H3 lysine-4 specific

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COMPASS component BRE2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COMPASS component SDC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COMPASS component SPP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COMPASS component SWD1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COMPASS component SWD3

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

6bx3__assembly_1__model_1

6bx3__assembly_1__model_1 | I(q)

6bx3__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 (6)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

7. Citations (1)