8jho

Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome

Method: ELECTRON MICROSCOPY

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

Histone H3

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H4 × 4 （A0A8J1LTD2） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136 Author chain a； PDBConstruct 1–135； UniProt 2–136 Author chain e； PDBConstruct 1–135； UniProt 2–136

Histone H4

Xenopus laevis

UniProt A0A8J1LTD2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J1LTD2_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 15–116 Author chain F； PDBConstruct 1–102； UniProt 15–116 Author chain b； PDBConstruct 1–102； UniProt 15–116 Author chain f； PDBConstruct 1–102； UniProt 15–116

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 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H4 × 4 （A0A8J1LTD2） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 2–130 Author chain G； PDBConstruct 1–129； UniProt 2–130 Author chain c； PDBConstruct 1–129； UniProt 2–130 Author chain g； PDBConstruct 1–129； UniProt 2–130

Histone H2B

Xenopus laevis

UniProt A0A8J0U496

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H4 × 4 （A0A8J1LTD2） Histone H2A × 4 （Q6AZJ8） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J0U496_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 Author chain d； PDBConstruct 1–122； UniProt 5–126 Author chain h； PDBConstruct 1–122； UniProt 5–126

Transcriptional regulatory protein SIN3

Saccharomyces cerevisiae

UniProt P22579

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H4 × 4 （A0A8J1LTD2） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Histone deacetylase RPD3 × 1 （P32561） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	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	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–1536； UniProt 1–1536

Histone deacetylase RPD3

Saccharomyces cerevisiae

UniProt P32561

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H4 × 4 （A0A8J1LTD2） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	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	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–433； UniProt 1–433

Chromatin modification-related protein EAF3

Saccharomyces cerevisiae

UniProt A0A8H4F719

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H4 × 4 （A0A8J1LTD2） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） RCO1 isoform 1 × 2 （A0A8H4BXB0） ZINC ION × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4F719_YEASX
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain M； PDBConstruct 1–401； UniProt 1–401 Author chain O； PDBConstruct 1–401； UniProt 1–401

RCO1 isoform 1

Saccharomyces cerevisiae

UniProt A0A8H4BXB0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 22 DNA 2	Histone H3 × 4 （A0A310TTQ1） Histone H4 × 4 （A0A8J1LTD2） Histone H2A × 4 （Q6AZJ8） Histone H2B × 4 （A0A8J0U496） Di-nucleosome template foward × 1 Di-nucleosome template reverse × 1 Transcriptional regulatory protein SIN3 × 1 （P22579） Histone deacetylase RPD3 × 1 （P32561） Chromatin modification-related protein EAF3 × 2 （A0A8H4F719） ZINC ION × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4BXB0_YEASX
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain N； PDBConstruct 1–684； UniProt 1–684 Author chain P； PDBConstruct 1–684； UniProt 1–684

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	8jho
Deposition date deposition_date	2023-05-25
Structure title title	Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome
Keywords keywords	HDAC, di-nucleosome, GENE REGULATION; GENE REGULATION
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.

8jho__assembly_1__model_1

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

Download this curve (.dat)

8jho__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8jho__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	91.31 Å
Rg (electron density)	90.23 Å
Total Rg	90.42 Å
Atom count	42813
Residues	4249
Excluded volume	720170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8jho__assembly_1__model_1`	24-meric （24）	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 (11)

Entity 1 Entity 1 polymer

Description description	Histone H3
Molecular weight formula_weight	15332.0 kDa
Mutation mutation	C110A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,a,e
Atom count atom_count	42813

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA

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	4

Polymer Polymer

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

Entity 3 Entity 3 polymer

Description description	Histone H2A
Molecular weight formula_weight	13978.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,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
Molecular weight formula_weight	13524.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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	Di-nucleosome template foward
Molecular weight formula_weight	107698.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATTCGATATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAAAGTACTGCCAGTTCTAGACTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGAT

Entity 6 Entity 6 polymer

Description description	Di-nucleosome template reverse
Molecular weight formula_weight	108485.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGTCTAGAACTGGCAGTACTTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGATATCGAAT

Entity 7 Entity 7 polymer

Description description	Transcriptional regulatory protein SIN3
Molecular weight formula_weight	175047.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKSYNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ

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 8 Entity 8 polymer

Description description	Histone deacetylase RPD3
Molecular weight formula_weight	48962.0 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	L

MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY

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	Chromatin modification-related protein EAF3
Molecular weight formula_weight	45266.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQKLGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKKSLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSLHPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVTKDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM

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	RCO1 isoform 1
Molecular weight formula_weight	78951.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIERSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPSEKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESNIRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTSNASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKCNQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHHCQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKITQIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIYFQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKKIIESKPKEELLKFLNIENPENQSE

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

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Resolution resolution	7.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	31310

Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome

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

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

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

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 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 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

Chromatin modification-related protein EAF3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RCO1 isoform 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

8jho__assembly_1__model_1

8jho__assembly_1__model_1 | I(q)

8jho__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source