SAXSdb — 9vkw

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1. Structure Basics

entry_id	9vkw
deposition_date	2025-06-24
title	Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A
keywords	NuA3, Cryo-EM, Histone, nucleosome, TRANSFERASE; TRANSFERASE
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	36.42 Å
rg_electron	35.64 Å
i0	357224000.00
molecular_weight	152740.0 kDa
excluded_volume	191170 Å³
envelope_volume	263430 Å³
shell_volume	60156 Å³
envelope_diameter	122.8 Å
shell_rg	43.06 Å
envelope_rg	35.58 Å
shape_rg	35.64 Å
total_rg	36.17 Å
total_atoms	10735
n_residues	1300
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	115.8 Å
rg_real	36.26 Å
rg_real_error	0.98 Å
i0_real	3.5720e+08
i0_real_error	6.3840e+06
rg_reciprocal	36.36 Å
i0_reciprocal	357300000.0000
total_estimate	0.8908
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.8 Å
skewness	0.216
kurtosis	-0.386
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	116900000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.894

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Histone acetyltransferase SAS3
formula_weight	97722.5 kDa
ec_number	2.3.1.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10735

MSLTANDESPKPKKNALLKNLEIDDLIHSQFVRSDTNGHRTTRRLFNSDASISHRIRGSVRSDKGLNKIKKGLISQQSKLASENSSQNIVNRDNKMGAVSFPIIEPNIEVSEELKVRIKYDSIKFFNFERLISKSSVIAPLVNKNITSSGPLIGFQRRVNRLKQTWDLATENMEYPYSSDNTPFRDNDSWQWYVPYGGTIKKMKDFSTKRTLPTWEDKIKFLTFLENSKSATYINGNVSLCNHNETDQENEDRKKRKGKVPRIKNKVWFSQIEYIVLRNYEIKPWYTSPFPEHINQNKMVFICEFCLKYMTSRYTFYRHQLKCLTFKPPGNEIYRDGKLSVWEIDGRENVLYCQNLCLLAKCFINSKTLYYDVEPFIFYILTEREDTENHPYQNAAKFHFVGYFSKEKFNSNDYNLSCILTLPIYQRKGYGQFLMEFSYLLSRKESKFGTPQKPLSDLGLLTYRTFWKIKCAEVLLKLRDSARRRSNNKNEDTFQQVSLNDIAKLTGMIPTDVVFGLEQLQVLYRHKTRSLSSLDDFNYIIKIDSWNRIENIYKTWSSKNYPRVKYDKLLWEPIILGPSFGINGMMNLEPTALADEALTNETMAPVISNNTHIENYNNSRAHNKRRRRRRRSSEHKTSKLHVNNIIEPEVPATDFFEDTVSSLTEYMCDYKNTNNDRLIYQAEKRVLESIHDRKGIPRSKFSTETHWELCFTIKNSETPLGNHAARRNDTGISSLEQDEVENDVDTELYVGENAKEDEDEDEDFTLDDDIEDEQISEENDEEEDTYEEDSDDDEDGKRKGQEQDENDIESHIRKERVRKRRKITLIEDDEE

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 2 polymer

description	NuA3 HAT complex component NTO1
formula_weight	86146.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MNRGSLDDGPKLREEKHFQDFYPDLNADTLLPFIVPLVETKDNSTDTDSDDISNRNNREIGSVKSVQTKELIFKGRVTTEPLVLKKNEVEFQKCKITTNELKGKKNPYCVRFNESFISRYYHINKVRNRKSYKQQQKEFDGVEAPYFTKFSSKEAPNITISTSTKSAIQKFASISPNLVNFKPQYDMDEQDELYLHYLNKRYFKDQMSHEIFEILMTTLETEWFHIEKHIPSTNSLIARHNILRDCKNYELYGSDDGTGLSMDQACAVCLGTDSDNLNTIVFCDGCDIAVHQECYGIIFIPEGKWLCRRCMISKNNFATCLMCPSHTGAFKQTDTGSWVHNICALWLPELYFSNLHYMEPIEGVQNVSVSRWKLNCYICKKKMGACIQCFQRNCFTAYHVTCARRAGLYMSKGKCTIQELASNQFSQKYSVESFCHKHAPRGWQTSIEGINKARKYFSLLSTLQTETPQHNEANDRTNSKFNKTIWKTPNQTPVAPHVFAEILQKVVDFFGLANPPAGAFDICKYWSMKRELTGGTPLTACFENNSLGSLTEEQVQTRIDFANDQLEDLYRLKELTTLVKKRTQASNSLSRSRKKVFDIVKSPQKYLLKINVLDIFIKSEQFKALERLVTEPKLLVILEKCKHCDFDTVQIFKEEIMHFFEVLETLPGASRILQTVSSKAKEQVTNLIGLIEHVDIKKLLSRDFIINDDKIEERPWSGPVIMEEEGLSDAEELSAGEHRMLKLILNSG

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 3 polymer

description	Protein YNG1
formula_weight	25391.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MEHLANENSDSDIRYSFLSTLDHLPCELIRSLRLMQTIDLFKNEEDEPGMERACRDLLLVATYINDLVDDQIHFLKQHKKELEIQKSVTKNFNSSLENIKSKLTLEEPGAYKEPKLLLKINLKKAKSRERKESITSPTIGINQGDVTEGNNNQEEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLKQAPKGKWYCSKDCKEIANQRSKSKRQKRRK

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 4 polymer

description	Transcription initiation factor TFIID subunit 14
formula_weight	27473.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MVATVKRTIRIKTQQHILPEVPPVENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHPTFANPNRTFTDPPFRIEEQGWGGFPLDISVFLLEKAGERKIPHDLNFLQESYEVEHVIQIPLNKPLLTEELAKSGSTEETTANTGTIGKRRTTTNTTAEPKAKRAKTGSASTVKGSVDLEKLAFGLTKLNEDDLVGVVQMVTDNKTPEMNVTNNVEEGEFIIDLYSLPEGLLKSLWDYVKKNTE

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 5 polymer

description	Chromatin modification-related protein EAF6
formula_weight	12915.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHGSKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Trichoplusia ni

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	ACETYL COENZYME *A
formula_weight	809.6 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.13 Å
resolution_method	—
num_particles	134246

fit	/app/data/saxs_computation/vk/9vkw/9vkw.fit
pddf	/app/data/pr_computation/vk/9vkw/9vkw.pr.out
profile	/app/data/saxs_computation/vk/9vkw/9vkw.dat

Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (7)

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 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)