6ven

Yeast COMPASS in complex with a ubiquitinated nucleosome

Method: ELECTRON MICROSCOPY

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

Histone H3.2

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103

Histone H2A type 1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 2–130 Author chain G； PDBConstruct 1–129； UniProt 2–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–122； UniProt 5–126 Author chain H； PDBConstruct 1–122； UniProt 5–126

Ubiquitin

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 5–80； UniProt 1–76

COMPASS component SWD3

Saccharomyces cerevisiae

UniProt P38123

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SWD3_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–315； UniProt 1–315

COMPASS component SWD1

Saccharomyces cerevisiae

UniProt P39706

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SWD1_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain M； PDBConstruct 1–426； UniProt 1–426

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

Saccharomyces cerevisiae

UniProt P38827

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SET1_YEAST
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain N； PDBConstruct 40–358； UniProt 762–1080

COMPASS component BRE2

Saccharomyces cerevisiae

UniProt P43132

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component SDC1 × 2 （Q03323） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRE2_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain O； PDBConstruct 1–505； UniProt 1–505

COMPASS component SDC1

Saccharomyces cerevisiae

UniProt Q03323

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SPP1 × 1 （Q03012） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDC1_YEAST
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain P； PDBConstruct 1–175； UniProt 1–175 Author chain Q； PDBConstruct 1–175； UniProt 1–175

COMPASS component SPP1

Saccharomyces cerevisiae

UniProt Q03012

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 16 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） 601 DNA (146-MER) × 1 601 DNA (146-MER) × 1 Ubiquitin × 1 （P0CG48） COMPASS component SWD3 × 1 （P38123） COMPASS component SWD1 × 1 （P39706） Histone-lysine N-methyltransferase, H3 lysine-4 specific × 1 （P38827） COMPASS component BRE2 × 1 （P43132） COMPASS component SDC1 × 2 （Q03323） ZINC ION × 1 S-ADENOSYLMETHIONINE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPP1_YEAST
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain R； PDBConstruct 40–391； UniProt 2–353

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	6ven
Deposition date deposition_date	2020-01-02
Structure title title	Yeast COMPASS in complex with a ubiquitinated nucleosome
Keywords keywords	Methylation, histone, transcription, ubiquitin, gene regulation, TRANSFERASE-STRUCTURAL PROTEIN-DNA complex; TRANSFERASE/STRUCTURAL PROTEIN/DNA
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.

6ven__assembly_1__model_1

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

Download this curve (.dat)

6ven__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ven__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.99 Å
Rg (electron density)	50.32 Å
Total Rg	50.57 Å
Atom count	24028
Residues	2558
Excluded volume	408720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ven__assembly_1__model_1`	octadecameric （18）	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 (15)

Entity 1 Entity 1 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15251.8 kDa
Mutation mutation	K4(NLE), M90(NLE), M120(NLE), G102A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	24028

ARTLQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVALFEDTNLCAIHAKRVTILPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	13978.2 kDa
Mutation mutation	G99R, A123S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13498.7 kDa
Mutation mutation	K120C, S30T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	601 DNA (146-MER)
Molecular weight formula_weight	44825.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	601 DNA (146-MER)
Molecular weight formula_weight	45305.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGA

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Ubiquitin
Molecular weight formula_weight	9036.4 kDa
Mutation mutation	G76C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC

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

Entity 8 Entity 8 polymer

Description description	COMPASS component SWD3
Molecular weight formula_weight	34786.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MFQFVTPVGTQNGLKATCAKISPDGQFLAITQGLNILIYDINRRTVSQTLVTSHARPFSELCWSPDGQCIATASDDFSVEIIHLSYGLLHTFIGHTAPVISLTFNRKGNLLFTSSMDESIKIWDTLNGSLMKTISAHSEAVVSVDVPMNDSSILSSGSYDGLIRIFDAETGHCLKTLTYDKDWKRENGVVPISQVKFSENARYLLVKSLDGVVKIWDCIGGCVVRTFQVQPLEKGVLHHSCGMDFLNPEDGSTPLVISGYENGDIYCWNSDTKSLLQLLDGSLYHHSSPVMSIHCFGNIMCSLALNGDCCLWRWV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 9 Entity 9 polymer

Description description	COMPASS component SWD1
Molecular weight formula_weight	48702.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MNILLQDPFAVLKEHPEKLTHTIENPLRTECLQFSPCGDYLALGCANGALVIYDMDTFRPICVPGNMLGAHVRPITSIAWSPDGRLLLTSSRDWSIKLWDLSKPSKPLKEIRFDSPIWGCQWLDAKRRLCVATIFEESDAYVIDFSNDPVASLLSKSDEKQLSSTPDHGYVLVCTVHTKHPNIIIVGTSKGWLDFYKFHSLYQTECIHSLKITSSNIKHLIVSQNGERLAINCSDRTIRQYEISIDDENSAVELTLEHKYQDVINKLQWNCILFSNNTAEYLVASTHGSSAHELYIWETTSGTLVRVLEGAEEELIDINWDFYSMSIVSNGFESGNVYVWSVVIPPKWSALAPDFEEVEENVDYLEKEDEFDEVDEAEQQQGLEQEEEIAIDLRTREQYDVRGNNLLVERFTIPTDYTRIIKMQSS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 10 Entity 10 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-4 specific
Molecular weight formula_weight	41508.5 kDa
EC 编号 ec_number	2.1.1.354
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MHHHHHHGSSDYKDHDGDYKDHDIDYKDDDDKENLYFQGMDLQNAIKDEEDMLILKQLLSTYTPTVTPETSAALEYKIWQSRRKVLEEEKASDWQIELNGTLFDSELQPGSSFKAEGFRKIADKLKINYLPHRRRVHQPLNTVNIHNERNEYTPELCQREESSNKEPSDSVPQEVSSSRDNRASNRRFQQDIEAQKAAIGTESELLSLNQLNKRKKPVMFARSAIHNWGLYALDSIAAKEMIIEYVGERIRQPVAEMREKRYLKNGIGSSYLFRVDENTVIDATKKGGIARFINHCCDPNCTAKIIKVGGRRRIVIYALRDIAASEELTYDYKFEREKDDEERLPCLCGAPNCKGFLN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 11 Entity 11 polymer

Description description	COMPASS component BRE2
Molecular weight formula_weight	58425.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MKLGIIPYQEGTDIVYKNALQGQQEGKRPNLPQMEATHQIKSSVQGTSYEFVRTEDIPLNRRHFVYRPCSANPFFTILGYGCTEYPFDHSGMSVMDRSEGLSISRDGNDLVSVPDQYGWRTARSDVCIKEGMTYWEVEVIRGGNKKFADGVNNKENADDSVDEVQSGIYEKMHKQVNDTPHLRFGVCRREASLEAPVGFDVYGYGIRDISLESIHEGKLNCVLENGSPLKEGDKIGFLLSLPSIHTQIKQAKEFTKRRIFALNSHMDTMNEPWREDAENGPSRKKLKQETTNKEFQRALLEDIEYNDVVRDQIAIRYKNQLFFEATDYVKTTKPEYYSSDKRERQDYYQLEDSYLAIFQNGKYLGKAFENLKPLLPPFSELQYNEKFYLGYWQHGEARDESNDKNTTSAKKKKQQQKKKKGLILRNKYVNNNKLGYYPTISCFNGGTARIISEEDKLEYLDQIRSAYCVDGNSKVNTLDTLYKEQIAEDIVWDIIDELEQIALQQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 12 Entity 12 polymer

Description description	COMPASS component SDC1
Molecular weight formula_weight	19466.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

MNESENSPQHNEVTVPMVEDTSSNADIPMEQIQREDNKNYDKHDNECFDMNGNHNNNSDNLQFDSVPSSATKDLKNIKSVTNQNVKIEESSSTNSVIEESSEPKISKLENVNLAATVGGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILKSGEKESNASK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 13 Entity 13 polymer

Description description	COMPASS component SPP1
Molecular weight formula_weight	45489.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MWSHPQFEKGGGSGGGSGGSSAWSHPQFEKGSENLYFQGSLPQWCPPHSTLKRNPTTGEDVYCICKRPDYGELMVGCDGCDDWFHFTCLHIPEQFKDLVFSFYCPYCQAGITGKNKDAIINGEGSLPKTLWKRKCRISDCYKPCLQDSKYCSEEHGREFVNDIWSRLKTDEDRAVVKKMVEQTGHIDKFKKFGQLDFIDNNIVVKTDDEKEIFDQIVVRDMTLKTLEDDLQEVQEISLPLFKKKLELLEVYLGWLDNVYTEMRKLDDDAASHVECGKEDSKGTKRKKKKNSSRSRARKNICGYCSTYERIPCSVEEFVRDFGSNEEATKIHEVCTKWKCNRHLDWVSTNQEQYLQQIDSLESMQERLQHLIQARKKQLNIQYYEEILRRGL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 non-polymer

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

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6venB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6venC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6venD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6venF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6venG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6venH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

▶

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	3.37 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	650847

Yeast COMPASS in complex with a ubiquitinated nucleosome

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

Histone H3.2

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 H4

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 H2A type 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

Histone H2B 1.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin

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

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

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