9CAE | pdb_00009cae

Cryo-EM structure of the reconstituted RuvBL lobe of the human TIP60 complex (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9CAE/pdb
EM Map EMD-45388: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens, Rhodococcus rhodochrous, Escherichia coli K-12
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-06-17 Released: 2025-06-18
Deposition Author(s): Louder, R.K., Park, G., Patel, A.B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60

Park, G., Patel, A.B., Wu, C., Louder, R.K.

To be published.

Macromolecule Content

Total Structure Weight: 962.14 kDa
Atom Count: 34,005
Modeled Residue Count: 4,289
Deposited Residue Count: 8,678
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1A-binding protein p400,E1A-binding protein p400/Haloalkane dehalogenase chimera	A	2,841	Homo sapiens, Rhodococcus rhodochrous This entity is chimeric	Mutation(s): 0 Gene Names: EP400, CAGH32, KIAA1498, KIAA1818, TNRC12, dhaA EC: 3.6.4 (PDB Primary Data), 3.8.1.5 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L91 (Homo sapiens) Explore Q96L91 Go to UniProtKB: Q96L91
PHAROS: Q96L91 GTEx: ENSG00000183495
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96L91
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 72 homolog	B	364	Homo sapiens	Mutation(s): 0 Gene Names: VPS72, TCFL1, YL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15906 (Homo sapiens) Explore Q15906 Go to UniProtKB: Q15906
PHAROS: Q15906 GTEx: ENSG00000163159
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15906
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Enhancer of polycomb homolog 1	C	263	Homo sapiens	Mutation(s): 0 Gene Names: EPC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2F5 (Homo sapiens) Explore Q9H2F5 Go to UniProtKB: Q9H2F5
PHAROS: Q9H2F5 GTEx: ENSG00000120616
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H2F5
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 1	D [auth E], F [auth G], H [auth I]	456	Homo sapiens	Mutation(s): 0 Gene Names: RUVBL1, INO80H, NMP238, TIP49, TIP49A EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens) Explore Q9Y265 Go to UniProtKB: Q9Y265
PHAROS: Q9Y265 GTEx: ENSG00000175792
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y265
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RuvB-like 2,RuvB-like 2/Maltose/maltodextrin-binding periplasmic protein chimera	E [auth F], G [auth H], I [auth J]	857	Homo sapiens, Escherichia coli K-12 This entity is chimeric	Mutation(s): 0 Gene Names: RUVBL2, INO80J, TIP48, TIP49B, CGI-46, malE, b4034, JW3994 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens) Explore Q9Y230 Go to UniProtKB: Q9Y230
PHAROS: Q9Y230 GTEx: ENSG00000183207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y230
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, cytoplasmic 1	J [auth L]	375	Homo sapiens	Mutation(s): 0 Gene Names: ACTB EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens) Explore P60709 Go to UniProtKB: P60709
PHAROS: P60709 GTEx: ENSG00000075624
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60709
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein 6A	K [auth M]	429	Homo sapiens	Mutation(s): 0 Gene Names: ACTL6A, BAF53, BAF53A, INO80K
UniProt & NIH Common Fund Data Resources
Find proteins for O96019 (Homo sapiens) Explore O96019 Go to UniProtKB: O96019
PHAROS: O96019 GTEx: ENSG00000136518
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96019
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA methyltransferase 1-associated protein 1	L [auth N]	467	Homo sapiens	Mutation(s): 0 Gene Names: DMAP1, KIAA1425
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF5 (Homo sapiens) Explore Q9NPF5 Go to UniProtKB: Q9NPF5
PHAROS: Q9NPF5 GTEx: ENSG00000178028
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPF5
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain M [auth E] SDF format, chain O [auth F] SDF format, chain Q [auth G] SDF format, chain S [auth H] SDF format, chain U [auth I] SDF format, chain W [auth J] SDF format, chain Y [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain M [auth E] MOL2 format, chain O [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain S [auth H] MOL2 format, chain U [auth I] MOL2 format, chain W [auth J] MOL2 format, chain Y [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain M [auth E] mmCIF format, chain O [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain S [auth H] mmCIF format, chain U [auth I] mmCIF format, chain W [auth J] mmCIF format, chain Y [auth L]	AA [auth M] M [auth E] O [auth F] Q [auth G] S [auth H] AA [auth M], M [auth E], O [auth F], Q [auth G], S [auth H], U [auth I], W [auth J], Y [auth L]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain AA [auth M] Focus chain M [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain W [auth J] Focus chain Y [auth L] Interactions & Density Focus chain AA [auth M] Focus chain M [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain W [auth J] Focus chain Y [auth L]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth M] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain R [auth G] SDF format, chain T [auth H] SDF format, chain V [auth I] SDF format, chain X [auth J] SDF format, chain Z [auth L] MOL2 format, chain BA [auth M] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain R [auth G] MOL2 format, chain T [auth H] MOL2 format, chain V [auth I] MOL2 format, chain X [auth J] MOL2 format, chain Z [auth L] mmCIF format, chain BA [auth M] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain R [auth G] mmCIF format, chain T [auth H] mmCIF format, chain V [auth I] mmCIF format, chain X [auth J] mmCIF format, chain Z [auth L]	BA [auth M] N [auth E] P [auth F] R [auth G] T [auth H] BA [auth M], N [auth E], P [auth F], R [auth G], T [auth H], V [auth I], X [auth J], Z [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain T [auth H] Focus chain V [auth I] Focus chain X [auth J] Focus chain Z [auth L] Interactions & Density Focus chain BA [auth M] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain T [auth H] Focus chain V [auth I] Focus chain X [auth J] Focus chain Z [auth L]