9LWI: Structural maintenance of chromosomes protein 6

The head region of HBx-Smc5/6 ubiquitination complex. Determined by electron microscopy at 3.12 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 3.12 Å
Organisms: Homo sapiens, Hepatitis B virus
Chains: 9
Atoms: 28,124
Mol. weight: 603.26 kDa
Ligands: ZN
Released: 29 Apr 2026

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

Secondary structure: helices and β-sheets

9LWI contains 122 α-helices and 169 β-strands across 9 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: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	45-52	8	1
β-strand	56	1	2
β-strand	59	1	2
β-strand	65-66	2	1
β-strand	71-75	5	3
α-helix	83-92	10
β-strand	110	1	2
α-helix	111	1
β-strand	116-125	10	1
α-helix	133-136	4
β-strand	139-147	9	1
β-strand	152-157	6	1
β-strand	163-165	3	1
α-helix	168-178	11
α-helix	191-194	4
α-helix	195-199	5
α-helix	203-214	12
α-helix	216-256	41
α-helix	893-951	59
β-strand	955	1	4
β-strand	958-961	4	5
β-strand	966-969	4	5
β-strand	972	1	4
α-helix	991-1006	16
β-strand	1011-1012	2	3
β-strand	1015	1	3
α-helix	1023-1039	17
β-strand	1044-1049	6	3
β-strand	1064-1066	3	3

Chain B: 13 helices, 100 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	6
β-strand	17-21	5	7
β-strand	30-34	5	7
β-strand	38-45	8	7
β-strand	48-56	9	7
β-strand	63-67	5	8
β-strand	70	1	9
β-strand	72	1	9
β-strand	76-80	5	8
β-strand	85-94	10	8
β-strand	97-107	11	8
β-strand	115	1	10
β-strand	122-124	3	11
β-strand	130-133	4	11
β-strand	136	1	10
β-strand	139-144	6	11
β-strand	151	1	8
β-strand	155-158	4	11
β-strand	164-169	6	12
β-strand	177-182	6	12
β-strand	189-196	8	12
β-strand	201-209	9	12
β-strand	218	1	13
β-strand	221	1	13
β-strand	229-232	4	13
β-strand	237-240	4	13
β-strand	247-248	2	13
α-helix	253-255	3
β-strand	258-263	6	14
β-strand	270-275	6	14
β-strand	279-289	11	14
α-helix	290	1
β-strand	295-307	13	14
β-strand	313-318	6	15
β-strand	321-325	5	15
β-strand	331-336	6	15
α-helix	342-344	3
β-strand	347-353	7	15
β-strand	359-363	5	16
β-strand	376-379	4	16
β-strand	386-391	6	16
β-strand	394	1	17
β-strand	396-402	7	18
β-strand	410-411	2	19
β-strand	424-428	5	19
β-strand	433-439	7	19
β-strand	442-445	4	19
β-strand	457-463	7	20
β-strand	467-472	6	20
β-strand	475-480	6	20
β-strand	485-491	7	20
β-strand	500-503	4	21
β-strand	507-512	6	21
β-strand	515-522	8	21
β-strand	525-533	9	21
β-strand	538-542	5	22
β-strand	555-560	6	22
β-strand	567-570	4	22
β-strand	576-578	3	22
β-strand	588-595	8	23
β-strand	600-606	7	23
β-strand	610-615	6	23
β-strand	616-617	2	24
β-strand	622-623	2	24
β-strand	629-630	2	23
β-strand	637-642	6	25
β-strand	647-652	6	25
β-strand	657-661	5	25
β-strand	666-670	5	25
β-strand	671	1	17
β-strand	678	1	18
β-strand	681-682	2	18
β-strand	690-694	5	18
β-strand	699-704	6	18
β-strand	711-716	6	16
β-strand	720-727	8	26
β-strand	732-744	13	26
β-strand	748-751	4	26
β-strand	762-765	4	26
α-helix	776-779	4
β-strand	785-795	11	26
β-strand	801-806	6	26
β-strand	811-819	9	27
β-strand	828-835	8	27
β-strand	846-853	8	27
β-strand	858-866	9	27
β-strand	873-876	4	28
β-strand	879-883	5	28
β-strand	888-893	6	28
β-strand	899-905	7	28
β-strand	913-917	5	29
β-strand	920-924	5	29
β-strand	930-936	7	29
β-strand	941-948	8	29
β-strand	954-958	5	30
β-strand	964-969	6	30
β-strand	973-979	7	30
α-helix	986-989	4
β-strand	991	1	29
β-strand	992-998	7	30
β-strand	1004-1009	6	6
β-strand	1025-1032	8	6
β-strand	1037-1042	6	6
α-helix	1045-1061	17
α-helix	1070-1074	5
α-helix	1083-1085	3
β-strand	1086	1	30
β-strand	1088-1090	3	6
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
α-helix	1123-1125	3
α-helix	1126-1137	12

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	58-59	2	31
α-helix	60-62	3
α-helix	89-98	10
α-helix	105-123	19
α-helix	127-134	8
β-strand	141-142	2	31

Chain D: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	26-53	28
α-helix	54-56	3
α-helix	65-79	15
α-helix	83-108	26
α-helix	116-126	11
α-helix	139-141	3
α-helix	147-160	14
α-helix	213-217	5
α-helix	218-219	2
α-helix	221-223	3
α-helix	255-268	14
α-helix	312-321	10

Chain E: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	82-99	18
β-strand	107	1	32
α-helix	108-114	7
α-helix	123-137	15
β-strand	140-144	5	33
β-strand	151	1	32
β-strand	152-156	5	33
α-helix	159-160	2
α-helix	177-188	12
β-strand	193-194	2	34
α-helix	195-203	9
β-strand	213	1	35
β-strand	217	1	35
α-helix	219-221	3
α-helix	222-226	5
α-helix	227-229	3
β-strand	233-237	5	34
β-strand	246-250	5	34
α-helix	252-257	6
α-helix	260-265	6
α-helix	279-293	15

Chain F: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
β-strand	27-29	3	36
α-helix	30-44	15
α-helix	49-50	2
α-helix	53-64	12
β-strand	69-75	7	36
β-strand	82-88	7	36
α-helix	94-98	5
α-helix	103-118	16
α-helix	126-131	6
α-helix	143-156	14
β-strand	159-162	4	37
β-strand	165-168	4	37
α-helix	170-183	14
β-strand	190	1	38
β-strand	197	1	38
β-strand	201-203	3	39
β-strand	210-212	3	39
α-helix	213-219	7
α-helix	240-245	6

Chain G: 38 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	58-73	16
α-helix	74-76	3
α-helix	83-93	11
α-helix	99-121	23
α-helix	128-152	25
α-helix	154-156	3
α-helix	157-161	5
α-helix	168-169	2
α-helix	170-181	12
α-helix	187-204	18
α-helix	211-223	13
α-helix	227	1
α-helix	228-232	5
α-helix	233-253	21
α-helix	256-276	21
α-helix	280-282	3
α-helix	283-294	12
α-helix	299-304	6
α-helix	307-313	7
α-helix	316-328	13
α-helix	332-353	22
α-helix	355-358	4
α-helix	361-378	18
α-helix	384-399	16
α-helix	404-417	14
α-helix	426-442	17
α-helix	446-462	17
α-helix	469-479	11
α-helix	485-515	31
β-strand	522-529	8	40
α-helix	534-535	2
α-helix	545-559	15
β-strand	565-580	16	40
β-strand	589-592	4	40
α-helix	593-601	9
α-helix	610-617	8
α-helix	621-629	9
β-strand	639-641	3	41
β-strand	654-656	3	41
β-strand	667	1	40
α-helix	670-674	5
α-helix	678-706	29
β-strand	710	1	42
α-helix	712-722	11
α-helix	729-741	13
β-strand	745-748	4	42
β-strand	751-757	7	42

Chain H: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-35	14	40
α-helix	36-37	2
α-helix	54-57	4
β-strand	70-72	3	43
β-strand	78-80	3	43
α-helix	87-90	4
β-strand	93	1	44
β-strand	100	1	44

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 6	A	protein	1091	Homo sapiens	Q96SB8 (AlphaFold model)
DNA damage-binding protein 1	B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein X	C	protein	154	Hepatitis B virus	Q2F514
EP300-interacting inhibitor of differentiation 3	D	protein	333	Homo sapiens	Q8N140 (AlphaFold model)
Non-structural maintenance of chromosomes element 3 homolog	E	protein	304	Homo sapiens	Q96MG7
Non-structural maintenance of chromosomes element 1 homolog	F	protein	266	Homo sapiens	Q8WV22
Cullin-4A	G	protein	760	Homo sapiens	Q13619
E3 ubiquitin-protein ligase RBX1	H	protein	108	Homo sapiens	P62877
Structural maintenance of chromosomes protein 5	I	protein	1101	Homo sapiens	Q8IY18

Sequence of entity 1 (A), FASTA

>9LWI_1 Structural maintenance of chromosomes protein 6 (chains A)
MAKRKEENFSSPKNAKRPRQEELEDFDKDGDEDECKGTTLTAAEVGIIESIHLKNFMCHS
MLGPFKFGSNVNFVVGNNGSGKSAVLTALIVGLGGRAVATNRGSSLKGFVKDGQNSADIS
ITLRNRGDDAFKASVYGNSILIQQHISIDGSRSYKLKSATGSVVSTRKEELIAILDHFNI
QVDNPVSVLTQEMSKQFLQSKNEGDKYKFFMKATQLEQMKEDYSYIMETKERTKEQIHQG
EERLTELKRQCVEKEERFQSIAGLSTMKTNLESLKHEMAWAVVNEIEKQLNAIRDNIKIG
EDRAARLDRKMEEQQVRLNEAEQKYKDIQDKLEKISEETNARAPECMALKADVVAKKRAY
NEAEVLYNRSLNEYKALKKDDEQLCKRIEELKKSTDQSLEPERLERQKKISWLKERVKAF
QNQENSVNQEIEQFQQAIEKDKEEHGKIKREELDVKHALSYNQRQLKELKDSKTDRLKRF
GPNVPALLEAIDDAYRQGHFTYKPVGPLGACIHLRDPELALAIESCLKGLLQAYCCHNHA
DERVLQALMKRFYLPGTSRPPIIVSEFRNEIYDVRHRAAYHPDFPTVLTALEIDNAVVAN
SLIDMRGIETVLLIKNNSVARAVMQSQKPPKNCREAFTADGDQVFAGRYYSSENTRPKFL
SRDVDSEISDLENEVENKTAQILNLQQHLSALEKDIKHNEELLKRCQLHYKELKMKIRKN
ISEIRELENIEEHQSVDIATLEDEAQENKSKMKMVEEHMEQQKENMEHLKSLKIEAENKY
DAIKFKINQLSELADPLKDELNLADSEVDNQKRGKRHYEEKQKEHLDTLNKKKRELDMKE
KELEEKMSQARQICPERIEVEKSASILDKEINRLRQKIQAEHASHGDREEIMRQYQEARE
TYLDLDSKVRTLKKFIKLLGEIMEHRFKTYQQFRRCLTLRCKLYFDNLLSQRAYCGKMNF
DHKNETLSISVQPGEGNKAAFNDMRALSGGERSFSTVCFILSLWSIAESPFRCLDEFDVY
MDMVNRRIAMDLILKMADSQRFRQFILLTPQSMSSLPSSKLIRILRMSDPERGQTTLPFR
PVTQEEDDDQR

Sequence of entity 2 (B), FASTA

>9LWI_2 DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C), FASTA

>9LWI_3 Protein X (chains C)
MAARLCCQLDPARDVLCLRPVGAESCGRPFSGSLGTLSSPSPSAVPTDHGAHLSLRGLPV
CAFSSAGPCALRFTSARRMETTVNAHQILPKVLHKRTLGLSAMSTTDLEAYFKDCLFKDW
EELGEEIRLKVFVLGGCRHKLVCAPAPCNFFTSA

Sequence of entity 4 (D), FASTA

>9LWI_4 EP300-interacting inhibitor of differentiation 3 (chains D)
MKMDVSVRAAGCSDDLSSGEADVDPKLLELTADEEKCRSIRRQYRQLMYCVRQNREDIVS
SANNSLTEALEEANVLFDGVSRTREAALDARFLVMASDLGKEKAKQLNSDMNFFNQLAFC
DFLFLFVGLNWMEGDPDKLSDCDDSIALSFWKAIEKEATSWMVKAETFHFVFGSFKLERS
APKPRLEHQKKVRKMEENGNMPTKLQKLDLSSYPEATEKNVERILGLLQTYFRKYPDTPV
SYFEFVIDPNSFSRTVENIFYVSFIVRDGFARIRLDEDRLPILEPMNVNQMGEGNDSSCH
GRKQGVISLTLQEWKNIVAAFEISEAMITYSSY

Sequence of entity 5 (E), FASTA

>9LWI_5 Non-structural maintenance of chromosomes element 3 homolog (chains E)
MLQKPRNRGRSGGQAERDRDWSHSGNPGASRAGEDARVLRDGFAEEAPSTSRGPGGSQGS
QGPSPQGARRAQAAPAVGPRSQKQLELKVSELVQFLLIKDQKKIPIKRADILKHVIGDYK
DIFPDLFKRAAERLQYVFGYKLVELEPKSNTYILINTLEPVEEDAEMRGDQGTPTTGLLM
IVLGLIFMKGNTIKETEAWDFLRRLGVYPTKKHLIFGDPKKLITEDFVRQRYLEYRRIPH
TDPVDYEFQWGPRTNLETSKMKVLKFVAKVHNQDPKDWPAQYCEALADEENRARPQPSGP
APSS

Sequence of entity 6 (F), FASTA

>9LWI_6 Non-structural maintenance of chromosomes element 1 homolog (chains F)
MQGSTRRMGVMTDVHRRFLQLLMTHGVLEEWDVKRLQTHCYKVHDRNATVDKLEDFINNI
NSVLESLYIEIKRGVTEDDGRPIYALVNLATTSISKMATDFAENELDLFRKALELIIDSE
TGFASSTNILNLVDQLKGKKMRKKEAEQVLQKFVQNKWLIEKEGEFTLHGRAILEMEQYI
RETYPDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP
KVFDPEKERESGVLKSNKKSLRSRQH

Sequence of entity 7 (G), FASTA

>9LWI_7 Cullin-4A (chains G)
MADEAPRKGSFSALVGRTNGLTKPAALAAAPAKPGGAGGSKKLVIKNFRDRPRLPDNYTQ
DTWRKLHEAVRAVQSSTSIRYNLEELYQAVENLCSHKVSPMLYKQLRQACEDHVQAQILP
FREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMGLELFRT
HIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDLQVYKDSFELKFLEETN
CLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEKQLLGEHLT
AILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYIKTFGTAIVINPEKDKD
MVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFINKRPNKPAELIAKHVDSKLRAG
NKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLK
HECGAAFTSKLEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLTVNILTMGYWPTYTPME
VHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLL
MFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEF
KHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELY
NQLKFPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVAG

Sequence of entity 8 (H), FASTA

>9LWI_8 E3 ubiquitin-protein ligase RBX1 (chains H)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 9 (I), FASTA

>9LWI_9 Structural maintenance of chromosomes protein 5 (chains I)
MATPSKKTSTPSPQPSKRALPRDPSSEVPSKRKNSAPQLPLLQSSGPFVEGSIVRISMEN
FLTYDICEVSPGPHLNMIVGANGTGKSSIVCAICLGLAGKPAFMGRADKVGFFVKRGCSR
GMVEIELFRASGNLVITREIDVAKNQSFWFINKKSTTQKIVEEKVAALNIQVGNLCQFLP
QDKVGEFAKLSKIELLEATEKSIGPPEMHKYHCELKNLREKEKQLETSCKEKTEYLQKMV
QRNERYKQDVERFYERKRHLDLIEMLEAKRPWVEYENVRQEYEEVKLVRDRVKEEVRKLK
EGQIPVTCRIEEMENERHNLEARIKEKATDIKEASQKCKQKQDVIERKDKHIEELQQALI
VKQNEELDRQRRIGNTRKMIEDLQNELKTTENCENLQPQIDAITNDLRRIQDEKALCEGE
IIDKRRERETLEKEKKSVDDHIVRFDNLMNQKEDKLRQRFRDTYDAVLWLRNNRDKFKQR
VCEPIMLTINMKDNKNAKYIENHIPSNDLRAFVFESQEDMEVFLKEVRDNKKLRVNAVIA
PKSSYADKAPSRSLNELKQYGFFSYLRELFDAPDPVMSYLCCQYHIHEVPVGTEKTRERI
ERVIQETRLKQIYTAEEKYVVKTSFYSNKVISSNTSLKVAQFLTVTVDLEQRRHLEEQLK
EIHRKLQAVDSGLIALRETSKHLEHKDNELRQKKKELLERKTKKRQLEQKISSKLGSLKL
MEQDTCNLEEEERKASTKIKEINVQKAKLVTELTNLIKICTSLHIQKVDLILQNTTVISE
KNKLESDYMAASSQLRLTEQHFIELDENRQRLLQKCKELMKRARQVCNLGAEQTLPQEYQ
TQVPTIPNGHNSSLPMVFQDLPNTLDEIDALLTEERSRASCFTGLNPTIVQEYTKREEEI
EQLTEELKGKKVELDQYRENISQVKERWLNPLKELVEKINEKFSNFFSSMQCAGEVDLHT
ENEEDYDKYGIRIRVKFRSSTQLHELTPHHQSGGERSVSTMLYLMALQELNRCPFRVVDE
INQGMDPINERRVFEMVVNTACKENTSQYFFITPKLLQNLPYSEKMTVLFVYNGPHMLEP
NTWNLKAFQRRRRRITFTQPS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Structural and functional insights into HBx-Smc6 targeting for HBV inhibition. Cheng, T., Zhou, J., Huang, W. et al. Cell Res (2026) 36:629-632. DOI 10.1038/s41422-026-01251-7 · PubMed

Other PDB entries of the same protein (UniProt Q96SB8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9LWJ 7.19 Å, The head-arm region of HBx-Smc5/6 ubiquitination complex
9LWL 7.25 Å, HBx-Smc5/6 ubiquitination complex
9LWK 7.32 Å, The hinge-arm region of HBx-Smc5/6 ubiquitination complex

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