9v2w

Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome

Method: ELECTRON MICROSCOPY

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

Transcriptional regulatory protein SIN3

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIN3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1096； UniProt 225–1320

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6AZJ8_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–107； UniProt 12–118 Author chain M； PDBConstruct 1–107； UniProt 12–118 Author chain O； PDBConstruct 1–107； UniProt 12–118 Author chain S； PDBConstruct 1–107； UniProt 12–118

Histone deacetylase RPD3

Saccharomyces cerevisiae S288C

UniProt P32561

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPD3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–378； UniProt 9–386

Histone H2B

Xenopus laevis

UniProt A0A8J1LZU9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J1LZU9_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–93； UniProt 32–124 Author chain N； PDBConstruct 1–93； UniProt 32–124 Author chain P； PDBConstruct 1–93； UniProt 32–124 Author chain T； PDBConstruct 1–93； UniProt 32–124

Transcriptional regulatory protein DEP1

Saccharomyces cerevisiae S288C

UniProt P31385

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEP1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–119； UniProt 177–295

Transcriptional regulatory protein SDS3

Saccharomyces cerevisiae S288C

UniProt P40505

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDS3_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–311； UniProt 14–324

Transcriptional regulatory protein SAP30

Saccharomyces cerevisiae S288C

UniProt P38429

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAP30_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–119； UniProt 73–191

Histone H3

Xenopus laevis

UniProt A0A310TTQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A310TTQ1_XENLA
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–98； UniProt 38–135 Author chain Q； PDBConstruct 1–98； UniProt 38–135 Author chain U； PDBConstruct 1–98； UniProt 38–135 Author chain W； PDBConstruct 1–98； UniProt 38–135

Transcriptional regulatory protein PHO23

Saccharomyces cerevisiae S288C

UniProt P50947

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHO23_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–105； UniProt 11–115

Transcriptional regulatory protein RXT2

Saccharomyces cerevisiae S288C

UniProt P38255

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Histone deacetylase complex subunit CTI6 × 1 （Q08923） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RXT2_YEAST
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–206； UniProt 169–374

Histone deacetylase complex subunit CTI6

Saccharomyces cerevisiae S288C

UniProt Q08923

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone H4 × 4 （P62799） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTI6_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 1–249； UniProt 243–491

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 24 DNA 2	Transcriptional regulatory protein SIN3 × 1 （P22579） Histone H2A × 4 （Q6AZJ8） Histone deacetylase RPD3 × 1 （P32561） Histone H2B × 4 （A0A8J1LZU9） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Histone H3 × 4 （A0A310TTQ1） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase complex subunit CTI6 × 1 （Q08923） DNA (329-MER) × 1 DNA (329-MER) × 1 ZINC ION × 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	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–79； UniProt 23–101 Author chain R； PDBConstruct 1–79； UniProt 23–101 Author chain V； PDBConstruct 1–79； UniProt 23–101 Author chain Z； PDBConstruct 1–79； UniProt 23–101

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	9v2w
Deposition date deposition_date	2025-05-21
Structure title title	Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome
Keywords keywords	Histone deacetylase complex, Histone modification, Rpd3L, Cryo-EM, di-nucleosome, GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/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.

9v2w__assembly_1__model_1

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

Download this curve (.dat)

9v2w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9v2w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	71.22 Å
Rg (electron density)	69.48 Å
Total Rg	69.85 Å
Atom count	39938
Residues	3911
Excluded volume	668540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9v2w__assembly_1__model_1`	26-meric （26）	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	Transcriptional regulatory protein SIN3
Molecular weight formula_weight	126786.0 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	39938

LSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALD

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Histone H2A
Molecular weight formula_weight	11722.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,M,O,S

RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP

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 3 Entity 3 polymer

Description description	Histone deacetylase RPD3
Molecular weight formula_weight	42747.4 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYA

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Histone H2B
Molecular weight formula_weight	10407.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,N,P,T

KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS

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 5 Entity 5 polymer

Description description	Transcriptional regulatory protein DEP1
Molecular weight formula_weight	14553.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

EQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRD

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 polymer

Description description	Transcriptional regulatory protein SDS3
Molecular weight formula_weight	35851.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

KDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRELTGQPPAPFRL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 7 Entity 7 polymer

Description description	Transcriptional regulatory protein SAP30
Molecular weight formula_weight	14210.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

TAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQ

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 8 Entity 8 polymer

Description description	Histone H3
Molecular weight formula_weight	11560.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,Q,U,W

KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER

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 9 Entity 9 polymer

Description description	Transcriptional regulatory protein PHO23
Molecular weight formula_weight	12360.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

LNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNT

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 10 Entity 10 polymer

Description description	Transcriptional regulatory protein RXT2
Molecular weight formula_weight	23359.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

ILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 11 Entity 11 polymer

Description description	Histone deacetylase complex subunit CTI6
Molecular weight formula_weight	28742.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

TFMAREEKQYQRMLEKALKESRRTSHQEDPESYENDADIYQGDTDNHNGTTRLQTDVMLTEGKPDSVTNDDMKESLRPSKEQSMEKTNDVEKEASQEKESSTGSAQDTEKTDEPILPLTSISSSEDDSRKASSRGSKRVSKPARKGNRTRRSNTSSDTNQNRRSADIGTDKPVKPRLPPQRTSLNEMRRRVSAILEFISRTQWELSEDQSDREEFVRFVENQHFVEKVDTIYNGYNESLSMMDDLTREL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 12 Entity 12 polymer

Description description	Histone H4
Molecular weight formula_weight	9066.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,R,V,Z

LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF

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 13 Entity 13 polymer

Description description	DNA (329-MER)
Molecular weight formula_weight	102177.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X

GACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGAAGACCACCATGGAATTCATGGCGGAAGCATGACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGA

Source Source

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

Entity 14 Entity 14 polymer

Description description	DNA (329-MER)
Molecular weight formula_weight	101038.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

TCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTCATGCTTCCGCCATGAATTCCATGGTGGTCTTCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTC

Source Source

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

Entity 15 Entity 15 non-polymer

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

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Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	205066

Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome

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

Transcriptional regulatory protein SIN3

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

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 deacetylase RPD3

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

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcriptional regulatory protein DEP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcriptional regulatory protein SDS3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcriptional regulatory protein SAP30

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 H3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcriptional regulatory protein PHO23

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcriptional regulatory protein RXT2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer