6chg

Crystal structure of the yeast COMPASS catalytic module

Method: X-RAY DIFFRACTION

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

KLLA0E24487p

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	KLLA0C10945p × 1 （Q6CTQ1） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （Q6CIT4） KLLA0A08800p × 1 （Q6CXF3） KLLA0E03521p × 2 （Q6CPN6） H3 × 1 S-ADENOSYLMETHIONINE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CLY5_KLULA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 16–327

KLLA0C10945p

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

UniProt Q6CTQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	KLLA0E24487p × 1 （Q6CLY5） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （Q6CIT4） KLLA0A08800p × 1 （Q6CXF3） KLLA0E03521p × 2 （Q6CPN6） H3 × 1 S-ADENOSYLMETHIONINE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CTQ1_KLULA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–405； UniProt 1–405

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

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

UniProt Q6CIT4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	KLLA0E24487p × 1 （Q6CLY5） KLLA0C10945p × 1 （Q6CTQ1） KLLA0A08800p × 1 （Q6CXF3） KLLA0E03521p × 2 （Q6CPN6） H3 × 1 S-ADENOSYLMETHIONINE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SET1_KLULA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–153； UniProt 848–1000

KLLA0A08800p

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

UniProt Q6CXF3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	KLLA0E24487p × 1 （Q6CLY5） KLLA0C10945p × 1 （Q6CTQ1） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （Q6CIT4） KLLA0E03521p × 2 （Q6CPN6） H3 × 1 S-ADENOSYLMETHIONINE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CXF3_KLULA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–439； UniProt 1–439

KLLA0E03521p

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

UniProt Q6CPN6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	KLLA0E24487p × 1 （Q6CLY5） KLLA0C10945p × 1 （Q6CTQ1） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （Q6CIT4） KLLA0A08800p × 1 （Q6CXF3） H3 × 1 S-ADENOSYLMETHIONINE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6CPN6_KLULA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–61； UniProt 74–134 Author chain F； PDBConstruct 1–61； UniProt 74–134

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	6chg
Deposition date deposition_date	2018-02-22
Structure title title	Crystal structure of the yeast COMPASS catalytic module
Keywords keywords	Histones, S-adenosylmethionine, Complex, enzyme, TRANSFERASE; TRANSFERASE
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.

6chg__assembly_1__model_1

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

Download this curve (.dat)

6chg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6chg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.80 Å
Rg (electron density)	44.02 Å
Total Rg	44.15 Å
Atom count	21029
Residues	1326
Excluded volume	189310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6chg__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 (9)

Entity 1 Entity 1 polymer

Description description	KLLA0E24487p
Molecular weight formula_weight	34794.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	21039

MLQFDKQVLPASGKISTSCQISPDGELIAICQNTDMLVYEISSSKMMKLTTTHKECINCLCWSPDSKCIASGSEDFTVEITHIIYGRIRRLMGHTAPVISICYNNKGNILCSSSMDESIKEWHVLSGTALKTMSAHSDAVVSIDIPKFDSSILSSGSYDGLIRIFDTESGHCLKTLTYDKDWIAEDGVVPISTVKFSRNGKFLLVKSLDNVVKLWEYTRGTVVRTFLWPHQETKAKLKYNCGLELIYPQGKDPLVISGNDSGSMCVWNVYSKNLVQKIDEKHRNSPLISISASYDKVATLSLNGECNLFRVH

Source Source

Source organism organism	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	KLLA0C10945p
Molecular weight formula_weight	47287.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSVPVIPYLDYDIVDLGSDIKKPDFPQLSESHRINEQQYYITEDTPLNKRNFMYQPCAANLMLDKLKYCGTDYFDKSSINLMDRSDKLAFSLDDHSVSVSENCGWRSVRSDVCMKEGKIYWEVEVKNVSDTSHIRCGISRREASTETPVGCDFYGYSIRDKGLQVIHEGRLHTVLKPHEMQAGDRIGFLLTLPSLQSQSEQAMDYSLKRIQELNNDDSRTNKRNKKFNKEFYKFLLRSCEPTNVVRDQIAIRYKNQLFYESTDYVKTTKPEYYDNRDDMQKFYELENSSFEVFVNGVSHGIAFEGLTPFLPPFSELQYNEKFYLHHWNKRNVTKGIEIRNKYVNNNRLGYYATLSSFQGGTASIITEAMELKFLPKDVDIKTLNDIYNEQIASDIVWDLIDEIDT

Source Source

Source organism organism	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-4 specific
Molecular weight formula_weight	17420.1 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	C

LSLNQLTKRKKPVTFARSAIHNWGLYALEPIAAKEMIIEYVGESIRQPVAEMREKRYIKSGIGSSYLFRIDENTVIDATKRGGIARFINHCCEPSCTAKIIKVDGRKRIVIYALRDIGTNEELTYDYKFERETDEGERLPCLCGAPSCKGFLN

Source Source

Source organism organism	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	KLLA0A08800p
Molecular weight formula_weight	49894.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MANLLLQDPFGVLKEYPEKLTHTLEVPVAAVCVKFSPRGDYLAVGCSNGAIIIYDMDSLKPIAMLGTHSGAHTRSVQSVCWSNDGRYLWSSGRDWYAKLWDMTQPTKCFQQYKFDGPLWSCHVVRWNVCIVTVVEEPTAYVLTLTDRQNAFHCFPLLEQDQDISGHGYTLVACPHPTIESIIITGTSKGWINAFQLDLESGFEDKIRCCYEEKIANANIKQIIISPSGTRIAINGSDRTIRQYQLIVEDNESEGGSSHSVSIELEHKYQDIINRLQWNTIFFSNHSGEYLVASAHGSSAHDLYLWETSSGSLVRVLEGADEELLDIDWNFYSMRIASNGFESGWVYMWSIVIPPKWSALAPDFEEVEENIDYQEKENEFDIMDDDNNLQAMTEAEEIAIDLCTPEKYDVRGNDISMPSFVIPIDYEGVIIQQHWAHQEQ

Source Source

Source organism organism	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	KLLA0E03521p
Molecular weight formula_weight	6900.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DRVDPVAMIGGSTTRRYLNEHVTKHLLEGMKLIAREKPEDPLRVLGQFLIDASEMNQKPSS

Source Source

Source organism organism	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	H3
Molecular weight formula_weight	535.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

RTMQ

Entity 7 Entity 7 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6chgC00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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Unit-cell length a length_a	163.839 Å
Unit-cell length b length_b	138.319 Å
Unit-cell length c length_c	136.133 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.985 Å
Low-resolution limit resolution_low	44.607 Å
R factor r_factor	0.2301
R_work r_work	0.2280
R_free r_free	0.2708

Crystal structure of the yeast COMPASS catalytic module

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

KLLA0E24487p

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

KLLA0C10945p

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

KLLA0A08800p

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

KLLA0E03521p

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

6chg__assembly_1__model_1

6chg__assembly_1__model_1 | I(q)

6chg__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 (9)

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

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)