8ga8

Structure of the yeast (HDAC) Rpd3L complex

Method: ELECTRON MICROSCOPY

▼

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

Transcriptional regulatory protein SDS3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDS3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–327； UniProt 1–327

Transcriptional regulatory protein SIN3

OrganismNot specified

UniProt P22579

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIN3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–1536； UniProt 1–1536 Author chain D； PDBConstruct 1–1536； UniProt 1–1536

Transcriptional regulatory protein SAP30

OrganismNot specified

UniProt P38429

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAP30_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain J； PDBConstruct 1–201； UniProt 1–201

Transcriptional regulatory protein PHO23

OrganismNot specified

UniProt P50947

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHO23_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain L； PDBConstruct 1–330； UniProt 1–330

Transcriptional regulatory protein RXT2

OrganismNot specified

UniProt P38255

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RXT2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–430； UniProt 1–430

Transcriptional regulatory protein DEP1

OrganismNot specified

UniProt P31385

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Histone deacetylase RPD3 × 2 （P32561） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEP1_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–405； UniProt 1–405

Histone deacetylase RPD3

OrganismNot specified

UniProt P32561

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Transcriptional regulatory protein RXT3 × 1 （Q07458） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPD3_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain B； PDBConstruct 1–433； UniProt 1–433 Author chain E； PDBConstruct 1–433； UniProt 1–433

Transcriptional regulatory protein RXT3

OrganismNot specified

UniProt Q07458

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Transcriptional regulatory protein SDS3 × 1 （P40505） Transcriptional regulatory protein SIN3 × 2 （P22579） Transcriptional regulatory protein SAP30 × 1 （P38429） Transcriptional regulatory protein PHO23 × 1 （P50947） Transcriptional regulatory protein RXT2 × 1 （P38255） Transcriptional regulatory protein DEP1 × 1 （P31385） Histone deacetylase RPD3 × 2 （P32561） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RXT3_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain K； PDBConstruct 1–294； UniProt 1–294

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ga8
Deposition date deposition_date	2023-02-22
Structure title title	Structure of the yeast (HDAC) Rpd3L complex
Keywords keywords	HDAC, Silencing, chromatin, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8ga8__assembly_1__model_1

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

Download this curve (.dat)

8ga8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ga8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.64 Å
Rg (electron density)	53.90 Å
Total Rg	53.95 Å
Atom count	22003
Residues	2675
Excluded volume	391620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ga8__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Transcriptional regulatory protein SDS3
Molecular weight formula_weight	37685.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	22011

MAIQKVSNKDLSRKDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRELTGQPPAPFRLRSD

Entity 2 Entity 2 polymer

Description description	Transcriptional regulatory protein SIN3
Molecular weight formula_weight	175047.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKSYNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ

Entity 3 Entity 3 polymer

Description description	Transcriptional regulatory protein SAP30
Molecular weight formula_weight	23064.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MARPVNTNAETESRGRPTQGGGYASNNNGSCNNNNGSNNNNNNNNNNNNNSNNSNNNNGPTSSGRTNGKQRLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQKKKFKMEFRG

Entity 4 Entity 4 polymer

Description description	Transcriptional regulatory protein PHO23
Molecular weight formula_weight	37081.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSSPANLFPGLNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNTEIPRGLRLGVDNHPAMHLHHELMEKIESKSNSKSSQALKSESRREAMAANRRQGEHYSASTHQQDDSKNDANYGGSRHESQDHTGNNTNSRKRANAANTNNADPETKKRKRRVATTAVSPSTISTATAVNNGRIGTSTASRGVSSVGNSNNSRISRPKTNDYGEPLYCYCNQVAYGEMVGCDGADCELEWFHLPCIGLETLPKGKWYCDDCKKKL

Entity 5 Entity 5 polymer

Description description	Transcriptional regulatory protein RXT2
Molecular weight formula_weight	48684.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MTIRSSMKNNAELESKSVLANESNIISTFTRRIIKEKSGNYQVLKRSLDGKLIYPEATGISSNRGNKLLQRSEVVTRRDLNNSKPMIEQTVFYNGSEHRLLQTNIVTDSRRKRIKFTPDINVEPVLVGDENDIDGSEKEDENITDEYYGEEDDDDLSKLVNVKEILTPILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYLGISDDDITIPVALRVVKRGLISATTNKTTNFEEEIENTMEDGVVDDNEPDEEANRA

Entity 6 Entity 6 polymer

Description description	Transcriptional regulatory protein DEP1
Molecular weight formula_weight	47035.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEKSLANLPELKYAPKLSSLVKQETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKSQELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVIPDVNYHVPIKLDNKTLSCITGYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIVDRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDFHQWAQ

Entity 7 Entity 7 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	nat
Copy count entity_count	2

Polymer Polymer

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

MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY

Entity 8 Entity 8 polymer

Description description	Transcriptional regulatory protein RXT3
Molecular weight formula_weight	33851.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MSVSEQDPNRAYRETQSQIYKLQETLLNSARTKNKQEEGQESNTHSFPEQYMHYQNGRNSAYDLPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDNTLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILVLRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYPSVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQRLDRDKPHEPNGYIKNLKWT

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8ga8B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	8ga8E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

▶

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	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	210993

Structure of the yeast (HDAC) Rpd3L complex

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

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 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

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

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

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

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

Transcriptional regulatory protein RXT3

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

8ga8__assembly_1__model_1

8ga8__assembly_1__model_1 | I(q)

8ga8__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer