9LPK: Human PADI6-UHRF1-UBE2D3 complex

Structure of human PADI6-UHRF1-UBE2D3 complex. Determined by electron microscopy at 3.03 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 6
Atoms: 16,278
Mol. weight: 368.92 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LPK contains 83 α-helices and 140 β-strands across 6 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.

Chains A and F: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	420-421	2
β-strand	429-430	2	1
α-helix	433-439	7
β-strand	449-452	4	1
β-strand	456-461	6	1
β-strand	471	1	1
β-strand	475-479	5	1
α-helix	504-509	6
β-strand	522-523	2	1
α-helix	527-529	3
α-helix	531-532	2
β-strand	533-537	5	1
α-helix	539-542	4
β-strand	553-568	16	1
β-strand	574-582	9	1
α-helix	587-588	2
α-helix	592-601	10
β-strand	606	1	1
α-helix	611-618	8

Chain B: 24 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	17
β-strand	23-28	6	18
β-strand	33-36	4	17
β-strand	47-52	6	18
β-strand	56-59	4	17
β-strand	64-65	2	17
β-strand	75	1	18
β-strand	82-87	6	17
β-strand	97-104	8	18
β-strand	111-122	12	18
β-strand	123-127	5	19
α-helix	144-146	3
β-strand	158-159	2	20
β-strand	161	1	19
α-helix	165-167	3
β-strand	180	1	21
α-helix	184-188	5
β-strand	190-197	8	19
α-helix	200-203	4
β-strand	207-211	5	20
α-helix	215-218	4
β-strand	220-225	6	19
β-strand	232	1	21
β-strand	233-237	5	19
β-strand	238	1	22
β-strand	241	1	22
β-strand	243-246	4	20
β-strand	252-261	10	19
β-strand	272-281	10	20
β-strand	291-302	12	20
β-strand	306-307	2	23
α-helix	313	1
β-strand	314-319	6	24
α-helix	328-338	11
β-strand	342-345	4	24
α-helix	356-359	4
β-strand	361-367	7	23
β-strand	372-378	7	23
α-helix	390-393	4
α-helix	395	1
β-strand	398	1	23
β-strand	401-402	2	23
β-strand	419-421	3	25
α-helix	422-424	3
β-strand	425-427	3	26
β-strand	430-432	3	26
β-strand	437-441	5	25
α-helix	454-462	9
β-strand	469-472	4	25
β-strand	476	1	27
α-helix	481-483	3
β-strand	485-489	5	28
β-strand	500-505	6	28
α-helix	507-519	13
β-strand	526	1	29
α-helix	533-538	6
β-strand	545	1	29
α-helix	546-550	5
α-helix	554-577	24
α-helix	581-583	3
β-strand	584-587	4	28
β-strand	591-594	4	27
α-helix	601-603	3
β-strand	609-612	4	27
β-strand	621-623	3	30
β-strand	626-630	5	30
β-strand	636-637	2	31
β-strand	640-641	2	31
α-helix	642-651	10
β-strand	657-661	5	30
α-helix	664-667	4
α-helix	669-670	2
β-strand	678-682	5	24
α-helix	683-685	3
α-helix	689-691	3

Chain C: 25 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	23-28	6	2
β-strand	33-36	4	3
β-strand	47-52	6	2
β-strand	56-60	5	3
β-strand	64-65	2	3
β-strand	75-76	2	2
β-strand	82-87	6	3
β-strand	97-104	8	2
β-strand	111-122	12	2
β-strand	123-128	6	4
α-helix	143-146	4
β-strand	158-159	2	5
β-strand	161	1	4
α-helix	165-167	3
β-strand	180	1	6
α-helix	184-188	5
β-strand	190-197	8	4
α-helix	200-203	4
β-strand	207-211	5	5
α-helix	215-218	4
β-strand	220-225	6	4
β-strand	232	1	6
β-strand	233-237	5	4
β-strand	238	1	7
β-strand	241	1	7
β-strand	243-246	4	5
β-strand	252-261	10	4
β-strand	272-281	10	5
β-strand	291-302	12	5
β-strand	306-307	2	8
α-helix	313	1
β-strand	314-320	7	9
α-helix	326-330	5
α-helix	331-338	8
β-strand	342-346	5	9
α-helix	356-359	4
β-strand	361-367	7	8
β-strand	372-378	7	8
α-helix	390-393	4
α-helix	395	1
β-strand	398	1	8
β-strand	401-402	2	8
β-strand	420-421	2	10
α-helix	422-424	3
β-strand	425-427	3	11
β-strand	430-432	3	11
β-strand	437-441	5	10
α-helix	454-462	9
β-strand	469-472	4	10
β-strand	476	1	12
α-helix	481-483	3
β-strand	485-489	5	13
β-strand	500-505	6	13
α-helix	507-519	13
β-strand	526	1	14
α-helix	533-538	6
β-strand	545	1	14
α-helix	546-550	5
α-helix	554-577	24
α-helix	581-583	3
β-strand	584-587	4	13
β-strand	591-594	4	12
α-helix	601-603	3
β-strand	609-612	4	12
β-strand	621-623	3	15
β-strand	626-630	5	15
β-strand	636-637	2	16
β-strand	640-641	2	16
α-helix	642-651	10
β-strand	657-661	5	15
α-helix	664-667	4
α-helix	669-670	2
β-strand	678-682	5	9
α-helix	683-685	3
α-helix	689-691	3

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	17-18	2
β-strand	23-26	4	36
β-strand	29-35	7	36
β-strand	36-38	3	37
α-helix	39-40	2
β-strand	49-51	3	37
β-strand	52-55	4	36
β-strand	66-69	4	36
β-strand	78	1	38
β-strand	83	1	36
β-strand	84	1	38
α-helix	87-90	4
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5

Chain E: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	17-18	2
β-strand	23-26	4	32
β-strand	29-35	7	32
β-strand	36-38	3	33
α-helix	39-40	2
β-strand	49-51	3	33
β-strand	54-55	2	32
β-strand	66-67	2	32
β-strand	68	1	34
β-strand	78	1	35
β-strand	83	1	34
β-strand	84	1	35
α-helix	87-90	4
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase UHRF1	A, F	protein	793	Homo sapiens	Q96T88 (AlphaFold model)
Protein-arginine deiminase type-6	B, C	protein	694	Homo sapiens	Q6TGC4 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D3	D, E	protein	147	Homo sapiens	P61077 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>9LPK_1 E3 ubiquitin-protein ligase UHRF1 (chains A, F)
MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD
YEVRLNDTIQLLVRQSLVLPHSTKERDSELSDTDSGCCLGQSESDKSSTHGEAAAETDSR
PADEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEE
DVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYD
AEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGP
SCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYC
PECRNDASEVVLAGERLRESKKKAKMASATSSSQRDWGKGMACVGRTKECTIVPSNHYGP
IPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDHGNFFTYTG
SGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVK
GGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTKEGKDRIKK
LGLTMQYPEGYLEALANREREKENSKREEEEQQEGGFASPRTGKGKWKRKSAGGGPSRAG
SPRRTSKKTKVEPYSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEE
TFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQT
VLNQLFPGYGNGR

Sequence of entity 2 (B, C), FASTA

>9LPK_2 Protein-arginine deiminase type-6 (chains B, C)
MVSVEGRAMSFQSIIHLSLDSPVHAVCVLGTEICLDLSGCAPQKCQCFTIHGSGRVLIDV
ANTVISEKEDATIWWPLSDPTYATVKMTSPSPSVDADKVSVTYYGPNEDAPVGTAVLYLT
GIEVSLEVDIYRNGQVEMSSDKQAKKKWIWGPSGWGAILLVNCNPADVGQQLEDKKTKKV
IFSEEITNLSQMTLNVQGPSCILKKYRLVLHTSKEESKKARVYWPQKDNSSTFELVLGPD
QHAYTLALLGNHLKETFYVEAIAFPSAEFSGLISYSVSLVEESQDPSIPETVLYKDTVVF
RVAPCVFIPCTQVPLEVYLCRELQLQGFVDTVTKLSEKSNSQVASVYEDPNRLGRWLQDE
MAFCYTQAPHKTTSLILDTPQAADLDEFPMKYSLSPGIGYMIQDTEDHKVASMDSIGNLM
VSPPVKVQGKEYPLGRVLIGSSFYPSAEGRAMSKTLRDFLYAQQVQAPVELYSDWLMTGH
VDEFMCFIPTDDKNEGKKGFLLLLASPSACYKLFREKQKEGYGDALLFDELRADQLLSNG
REAKTIDQLLADESLKKQNEYVEKCIHLNRDILKTELGLVEQDIIEIPQLFCLEKLTNIP
SDQQPKRSFARPYFPDLLRMIVMGKNLGIPKPFGPQIKGTCCLEEKICCLLEPLGFKCTF
INDFDCYLTEVGDICACANIRRVPFAFKWWKMVP

Sequence of entity 3 (D, E), FASTA

>9LPK_3 Ubiquitin-conjugating enzyme E2 D3 (chains D, E)
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDRDKYNRISREWTQKYAM

Primary citation

The maternal PADI6-UHRF1-UBE2D complex regulates ubiquitination during oocyte maturation and embryogenesis. Li, J., Lu, Y., Xia, Z. et al. Nat Struct Mol Biol (2026) 33:512-524. DOI 10.1038/s41594-026-01758-y · PubMed

Other PDB entries of the same protein (UniProt Q96T88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W92 1.3 Å, Human UHRF1 TTD domain
6VYJ 1.39 Å, Human UHRF1 TTD domain in complex with a fragment
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
3ZVZ 1.45 Å, PHD finger of human UHRF1
7FB7 1.45 Å, Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine
8XV6 1.6 Å, Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)
6B9M 1.68 Å, Crystal structure of UHRF1 TTD domain in complex with the polybasic region
6IIW 1.7 Å, Crystal structure of human UHRF1 PHD finger in complex with PAF15
3BI7 1.7 Å, Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1
5YYA 1.7 Å, Crystal structure of Tandem Tudor Domain of human UHRF1
6VCS 1.7 Å, SRA domain of UHRF1 in complex with DNA
3FL2 1.75 Å, Crystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1

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