9IMZ: Codanin-1

CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate histone supply. Determined by electron microscopy at 3.75 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.75 Å
Organism: Homo sapiens
Chains: 5
Atoms: 12,167
Mol. weight: 330.94 kDa
Released: 19 Mar 2025

Explore 9IMZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IMZ contains 88 α-helices and 39 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 38 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
α-helix	15-22	8
α-helix	34-40	7
α-helix	43-45	3
α-helix	49-61	13
α-helix	66-67	2
β-strand	195-197	3	1
β-strand	200	1	2
α-helix	249-261	13
α-helix	293-295	3
α-helix	300-314	15
α-helix	321-331	11
α-helix	363-374	12
α-helix	378-381	4
α-helix	386-393	8
α-helix	398-400	3
α-helix	403-415	13
α-helix	451-466	16
α-helix	477-481	5
α-helix	484-495	12
α-helix	498-514	17
α-helix	539-549	11
α-helix	560-562	3
α-helix	566-568	3
α-helix	569-578	10
α-helix	581-599	19
α-helix	625-644	20
α-helix	646-648	3
α-helix	660-668	9
α-helix	671-672	2
α-helix	676-685	10
α-helix	689-699	11
α-helix	700-702	3
α-helix	707-709	3
α-helix	712-726	15
α-helix	739-752	14
α-helix	762-765	4
α-helix	792-798	7
α-helix	800-803	4
α-helix	804-814	11
β-strand	826-827	2	3
β-strand	830-832	3	4

Chain B: 36 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	15-23	9
α-helix	34-40	7
α-helix	43-45	3
α-helix	49-60	12
α-helix	293-295	3
α-helix	300-314	15
α-helix	321-332	12
α-helix	363-374	12
α-helix	378-381	4
α-helix	386-394	9
α-helix	396-401	6
α-helix	403-412	10
α-helix	451-469	19
α-helix	477-481	5
α-helix	484-495	12
α-helix	498-514	17
α-helix	539-546	8
α-helix	547-550	4
α-helix	560-562	3
α-helix	566-568	3
α-helix	569-578	10
α-helix	581-598	18
α-helix	625-644	20
α-helix	653-655	3
α-helix	658-667	10
α-helix	676-685	10
α-helix	689-700	12
α-helix	706-709	4
α-helix	712-724	13
α-helix	732-735	4
α-helix	739-752	14
α-helix	760-763	4
α-helix	792-798	7
α-helix	800-803	4
α-helix	804-814	11
β-strand	827	1	5
β-strand	830	1	6

Chain C: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	4
β-strand	16-17	2	3
α-helix	21	1
β-strand	22-30	9	4
β-strand	38-45	8	3
α-helix	51-53	3
β-strand	54-62	9	3
β-strand	68-76	9	4
α-helix	77-80	4
β-strand	91-101	11	3
β-strand	104-117	14	3
α-helix	120-124	5
β-strand	135-139	5	3
β-strand	145-148	4	3

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	6
β-strand	16-17	2	7
α-helix	21	1
β-strand	22-30	9	6
β-strand	39-44	6	7
α-helix	51-53	3
β-strand	55-61	7	7
β-strand	62	1	5
β-strand	68-76	9	6
α-helix	77-80	4
α-helix	81-83	3
β-strand	91-101	11	7
β-strand	104-117	14	7
α-helix	120-124	5
β-strand	135-139	5	7
β-strand	145-148	4	7

Chain E: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	2
β-strand	16-17	2	1
α-helix	21	1
β-strand	22-30	9	2
β-strand	34	1	8
α-helix	37	1
β-strand	38-44	7	1
β-strand	55-62	8	1
β-strand	65	1	8
β-strand	68	1	2
β-strand	71-76	6	2
α-helix	77-80	4
α-helix	86-89	4
β-strand	91-101	11	1
β-strand	104-116	13	1
α-helix	120-124	5
β-strand	136-148	13	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Codanin-1	A, B	protein	1241	Homo sapiens	Q8IWY9 (AlphaFold model)
Histone chaperone ASF1A	C, D, E	protein	174	Homo sapiens	Q9Y294 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9IMZ_1 Codanin-1 (chains A, B)
MAAVLESLLREEVSVAAVVRWIARSTQGSEDNAGEAAALSSLRALRKEFVPFLLNFLREQ
SSRVLPQGPPTPAKTPGASAALPGRPGGPPRGSRGARSQLFPPTEAQSTAAEAPLARRGG
RRRGPGPARERGGRGLEEGVSGESLPGAGGRRLRGSGSPSRPSLTLSDPPNLSNLEEFPP
VGSVPPGPTGTKPSRRINPTPVSEERSLSKPKTCFTSPPISCVPSSQPSALDTSPWGLGL
PPGCRSLQEEREMLRKERSKQLQQSPTPTCPTPELGSPLPSRTGSLTDEPADPARVSSRQ
RLELVALVYSSCIAENLVPNLFLELFFVFQLLTARRMVTAKDSDPELSPAVLDSLESPLF
QSIHDCVFFAVQVLECHFQVLSNLDKGTLKLLAENERLLCFSPALQGRLRAAYEGSVAKV
FLVMPPSTQAVSFQPETDNRANFSSDRAFHTFKKQRDVFYEVLREWEDHHEEPGWDFEKG
LGSRIRAMMGQLSAACSHSHFVRLFQKQLLQMCQSPGGAGGTVLGEAPDVLSMLGADKLG
RLWRLQERLMAPQSSGGPCPPPTFPGCQGFFRDFILSASSFQFNQHLMDSLSLKIQELNG
LALPQHEPNDEDGESDVDWQGERKQFAVVLLSLRLLAKFLGFVAFLPYRGPEPPPTGELQ
DSILALRSQVPPVLDVRTLLQRGLQARRAVLTVPWLVEFLSFADHVVPLLEYYRDIFTLL
LRLHRSLVLSQESEGKMCFLNKLLLLAVLGWLFQIPTVPEDLFFLEEGPSYAFEVDTVAP
EHGLDNAPVVDQQLLYTCCPYIGELRKLLASWVSGSSGRSGGFMRKITPTTTTSLGAQPS
QTSQGLQAQLAQAFFHNQPPSLRRTVEFVAERIGSNCVKHIKATLVADLVRQAESLLQEQ
LVTQGEEGGDPAQLLEILCSQLCPHGAQALALGREFCQRKSPGAVRALLPEETPAAVLSS
AENIAVGLATEKACAWLSANITALIRREVKAAVSRTLRAQGPEPAARGERRGCSRACEHH
APLPSHLISEIKDVLSLAVGPRDPDEGVSPEHLEQLLGQLGQTLRCRQFLCPPAEQHLAK
CSVELASLLVADQIPILGPPAQYRLERGQARRLLHMLLSLWKEDFQGPVPLQLLLSPRNV
GLLADTRPREWDLLLFLLRELVEKGLMGRMEIEACLGSLHQAQWPGDFAEELATLSNLFL
AEPHLPEPQLRACELVQPNRGTVLAQSLEACGTKLENLYFQ

Sequence of entity 2 (C, D, E), FASTA

>9IMZ_2 Histone chaperone ASF1A (chains C, D, E)
GSMAKVQVNNVVVLDNPSPFYNPFQFEITFECIEDLSEDLEWKIIYVGSAESEEYDQVLD
SVLVGPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQEFIRVGYYVNNEYT
ETELRENPPVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESSNPNLQS

Primary citation

CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply. Jeong, T.K., Frater, R.C.M., Yoon, J. et al. Nat Commun (2025) 16:2181-2181. DOI 10.1038/s41467-025-56976-7 · PubMed

Other PDB entries of the same protein (UniProt Q8IWY9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CVC 3.5 Å, CDAN1 dimer with three ASF1A

Browse structure collections

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