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9v2v

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

Method: ELECTRON MICROSCOPY D_max: 217.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v2v
deposition_date	2025-05-21
title	Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
keywords	;Histone deacetylase complex, Histone modification, Rpd3L, Cryo-EM, mono-nucleosome, GENE REGULATION/DNA, GENE REGULATION-DNA complex ;; GENE REGULATION/DNA
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	67.27 Å
rg_electron	67.11 Å
i0	4320480000.00
molecular_weight	491830.0 kDa
excluded_volume	589520 Å³
envelope_volume	942530 Å³
shell_volume	119820 Å³
envelope_diameter	238.9 Å
shell_rg	64.05 Å
envelope_rg	66.22 Å
shape_rg	67.05 Å
total_rg	67.25 Å
total_atoms	34241
n_residues	3721
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	217.0 Å
rg_real	67.51 Å
rg_real_error	2.05 Å
i0_real	4.3190e+09
i0_real_error	9.1600e+07
rg_reciprocal	66.21 Å
i0_reciprocal	4310000000.0000
total_estimate	0.8268
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	66.0 Å
skewness	0.527
kurtosis	-0.271
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0004
highest_alpha	198700000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.100

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4. Crystallography & Experiment

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5. Entities & Polymer Info (16)

Entity 1 polymer

description	Transcriptional regulatory protein SIN3
formula_weight	80758.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	34241

LNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALP

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 2 polymer

description	Histone deacetylase RPD3
formula_weight	43524.3 kDa
ec_number	3.5.1.98
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

DPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNH

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 3 polymer

description	Transcriptional regulatory protein DEP1
formula_weight	14553.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

EQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRD

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 4 polymer

description	Transcriptional regulatory protein SDS3
formula_weight	35851.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

KDKRRFNIESKVNKIYQNFYSERDNQYKDRLTALQTDLTSLHQGDNGQYARQVRDLEEERDLELVRLRLFEEYRVSRSGIEFQEDIEKAKAEHEKLIKLCKERLYSSIEQKIKKLQEERLLMDVANVHSYAMNYSRPQYQKNTRSHTVSGWDSSSNEYGRDTANESATDTGAGNDRRTLRRRNASKDTRGNNNNQDESDFQTGNGSGSNGHGSRQGSQFPHFNNLTYKSGMNSDSDFLQGINEGTDLYAFLFGEKNPKDNANGNEKKKNRGAQRYSTKTAPPLQSLKPDEVTEDISLIRELTGQPPAPFRL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 5 polymer

description	Transcriptional regulatory protein SAP30
formula_weight	14480.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

RLTAAQQQYIKNLIETHITDNHPDLRPKSHPMDFEEYTDAFLRRYKDHFQLDVPDNLTLQGYLLGSKLGAKTYSYKRNTQGQHDKRIHKRDLANVVRRHFDEHSIKETDCIPQFIYKVKNQ

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 6 polymer

description	Transcriptional regulatory protein RXT3
formula_weight	23933.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

LPNVSSQSVLAFTEKHYPNKLKNLGTLYYNRFKEGSFDEDSTSYSDRHSFPYNLYDNTLPPPFLPAIGIQNINNIATLKITYEDIQASFNNIESPRKRNNEIWGCDIYSDDSDPILVLRHCGFKIGAPSGGSFHKLRRTPVNVTNQDNVTGNLPLLEGTPFDLEVELLFLPTLQKYPSVKRFDITSREWGSEATVIHDGLSYGIYSIVIKQ

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 7 polymer

description	Transcriptional regulatory protein PHO23
formula_weight	12360.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

LNDITDVLEEFPLATSRYLTLLHEIDAKCVHSMPNLNERIDKFLKKDFNKDHQTQVRLLNNINKIYEELMPSLEEKMHVSSIMLDNLDRLTSRLELAYEVAIKNT

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 8 polymer

description	Transcriptional regulatory protein RXT2
formula_weight	24683.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

SKLVNVKEILTPILSLGDIINHKTISRTFSSPILKNLALQIILMIEKEQMSVVRYSQFLEVFLGDHPEPIYESNLNLPSYNHNLTLPEDRGASDEDDINNKNNINEVNSNSLSTEAGHINNGMEEFGEEDPFFALPRLEQSNALLSLLPSSSGSASISTLTAAEQQQLNEEIESARQLSQIALQRNKEFIRNLQKIRKSVIKANRIRGRILNWSREYL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 9 polymer

description	Histone deacetylase complex subunit CTI6
formula_weight	28742.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

TFMAREEKQYQRMLEKALKESRRTSHQEDPESYENDADIYQGDTDNHNGTTRLQTDVMLTEGKPDSVTNDDMKESLRPSKEQSMEKTNDVEKEASQEKESSTGSAQDTEKTDEPILPLTSISSSEDDSRKASSRGSKRVSKPARKGNRTRRSNTSSDTNQNRRSADIGTDKPVKPRLPPQRTSLNEMRRRVSAILEFISRTQWELSEDQSDREEFVRFVENQHFVEKVDTIYNGYNESLSMMDDLTREL

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 10 polymer

description	Histone H2A
formula_weight	11722.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	O,S

RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 11 polymer

description	Histone H2B
formula_weight	10407.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	P,T

KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 12 polymer

description	Histone H3
formula_weight	11560.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Q,U

KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 13 polymer

description	Histone H4
formula_weight	9066.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	R,V

LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	Escherichia coli

Entity 14 polymer

description	DNA (155-MER)
formula_weight	48115.7 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	X

TCTAGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGG

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 15 polymer

description	DNA (155-MER)
formula_weight	47577.3 kDa
src_method	man
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

CCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCTAGA

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 16 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.00 Å
resolution_method	—
num_particles	451544

fit	/app/data/saxs_computation/v2/9v2v/9v2v.fit
pddf	/app/data/pr_computation/v2/9v2v/9v2v.pr.out
profile	/app/data/saxs_computation/v2/9v2v/9v2v.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (16)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 polymer

Polymer

Source

Entity 10 polymer

Polymer

Source

Entity 11 polymer

Polymer

Source

Entity 12 polymer

Polymer

Source

Entity 13 polymer

Polymer

Source

Entity 14 polymer

Polymer

Source

Entity 15 polymer

Polymer

Source

Entity 16 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)