8T8E: Smc5/6 5mer

cryoEM structure of Smc5/6 5mer. Determined by electron microscopy at 3.3 Å resolution. Released 15 Nov 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae W303
Chains: 3
Atoms: 8,755
Mol. weight: 246.12 kDa
Released: 15 Nov 2023

Explore 8T8E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T8E contains 60 α-helices and 24 β-strands across 3 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: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	77-78	2
β-strand	82-88	7	1
β-strand	97-99	3	1
β-strand	104	1	2
β-strand	107	1	3
α-helix	115-124	10
α-helix	144	1
β-strand	150-157	8	1
α-helix	166-169	4
β-strand	172-179	8	1
α-helix	184-185	2
β-strand	186	1	1
β-strand	189-190	2	1
β-strand	196-198	3	1
α-helix	201-210	10
β-strand	221	1	4
α-helix	224-230	7
α-helix	236-246	11
α-helix	252-255	4
α-helix	259-262	4
α-helix	952-958	7
α-helix	961-965	5
α-helix	974-980	7
β-strand	989-995	7	5
β-strand	1000-1006	7	5
β-strand	1014-1015	2	5
α-helix	1021-1036	16
β-strand	1043-1044	2	6
β-strand	1045	1	4
β-strand	1047	1	3
α-helix	1055-1070	16
β-strand	1076-1077	2	6
β-strand	1080	1	3
β-strand	1096	1	2
β-strand	1099	1	3

Chain B: 16 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	209-219	11
α-helix	246-253	8
α-helix	271-273	3
β-strand	281	1	8
α-helix	284-291	8
α-helix	292-294	3
α-helix	301-315	15
α-helix	318-321	4
α-helix	330-336	7
α-helix	340-345	6
α-helix	357-362	6
α-helix	367-369	3
α-helix	370-377	8
α-helix	388-397	10
α-helix	409-415	7
α-helix	433-439	7
α-helix	453-459	7

Chain C: 29 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
α-helix	26-40	15
α-helix	44-52	9
α-helix	63-65	3
α-helix	72-75	4
α-helix	85-90	6
α-helix	100-108	9
α-helix	112-115	4
α-helix	125-139	15
β-strand	198	1	7
β-strand	201	1	7
α-helix	205-208	4
α-helix	216-223	8
α-helix	230-233	4
α-helix	234-236	3
α-helix	241-258	18
α-helix	269-272	4
α-helix	273-275	3
α-helix	280-286	7
α-helix	297-300	4
α-helix	314-317	4
β-strand	336	1	8
α-helix	340-346	7
α-helix	348-355	8
α-helix	389-391	3
α-helix	395-402	8
α-helix	414-429	16
α-helix	439-441	3
α-helix	445-457	13
α-helix	472-496	25
α-helix	506-527	22
α-helix	539-546	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 6	A	protein	1114	Saccharomyces cerevisiae W303	Q12749 (AlphaFold model)
Non-structural maintenance of chromosome element 5	C	protein	556	Saccharomyces cerevisiae W303	Q03718 (AlphaFold model)
DNA repair protein KRE29	B	protein	464	Saccharomyces cerevisiae W303	P40026 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8T8E_1 Structural maintenance of chromosomes protein 6 (chains A)
MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFR
SSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILT
AITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIK
RDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY
SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDL
NERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTT
IEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKT
IAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERES
ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLV
TIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDY
SKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMAL
SLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE
EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQA
IASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKY
KDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEI
KRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR
DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLS
GGEKSFSQMALLLATWKPMRSRIIALDQFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN

Sequence of entity 2 (C), FASTA

>8T8E_2 Non-structural maintenance of chromosome element 5 (chains C)
MDGALINSVLYVSPRNGAHYFVELTEKHLLAFEMLNSMCLLENYDHVLLFLECQFGKSHN
LAVIPFDIILVLFTLSTLSEYYKEPILRANDPYNTSRETLSRRALKLLQKYLAILKEFDS
EQYNLYDLELLRCQFFLAIDTLTPKKQKWGFDRFRRTKSESGVTYRQNASVDPELDQAKT
FKNPYRSYISCLEQRNTILGNRLLNLKLNEPGEFINMILWTLSNSLQESTPLFLSSHEIW
MPLLEILIDLFSCRQDYFIQHEVAQNVSKSLFVQRLSESPLAVFFESLNTRNFANRFSEY
VFLNCDYKLPSDNYATPVHPVYNGENTIVDTYIPTIKCSPLYKSQKSLALRRKLIGSCFK
LLLRVPDGHRLITPRIVADDVIQGISRTLASFNDILQFKKFFMTENLSQESYFIPLLAEG
TLSEILKDTQECVVILTLVENLSDGVSFCNEVIGLVKSKCFAFTEQCSQASYEEAVLNIE
KCDVCLLVLLRYLLHLIGTEAILDAKEQLEMLHAIEKNDSGRRQWAKALNLGNDPPLLYP
IVSQMFGVHDKSVIIE

Sequence of entity 3 (B), FASTA

>8T8E_3 DNA repair protein KRE29 (chains B)
MGSVNSSPNEEFETVPDSQISGFDSPLIPTSVGSYFRDDDDDEKVHPNFISDPENDSLNS
DEEFSSLENSDLNLSGAKAESGDDFDPILKRTIISKRKAPSNNEDEEIVKTPRKLVNYVP
LKIFNLGDSFDDTITTTVAKLQDLKKEILDSPRSNKSIVITSNTVAKSELQKSIKFSGSI
PEIYLDVVTKETISDKYKDWHFISKNCHYEQLMDLEMKDTAYSFLFGSSRSQGKVPEFVH
LKCPSITNLLVLFGVNQEKCNSLKINYEKKENSRYDNLCTIFPVNKMLKFLMYFYSDDDN
DDVREFFLKAFICLILDRKVFNAMESDHRLCFKVLELFNEAHFINSYFEIVDKNDFFLHY
RLLQIFPHLQSALLRRRFSEKQGRTETIQQNIIKEFNEFFDCKNYKNLLYFILTMYGSKF
IPFGPKCQVTEYFKDCILDISNETTNDVEISILKGILNLFSKIR

Primary citation

Molecular basis for Nse5-6 mediated regulation of Smc5/6 functions. Li, S., Yu, Y., Zheng, J. et al. Proc Natl Acad Sci U S A (2023) 120:e2310924120-e2310924120. DOI 10.1073/pnas.2310924120 · PubMed

Other PDB entries of the same protein (UniProt Q12749 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HQS 3.2 Å, Cryo-EM structure of 8-subunit Smc5/6 head region
7TVE 3.8 Å, ATP and DNA bound SMC5/6 core complex
8T8F 4.8 Å, Smc5/6 8mer
8WJN 5.58 Å, Cryo-EM structure of 6-subunit Smc5/6 head region
7YQH 5.6 Å, Cryo-EM structure of 8-subunit Smc5/6
8I4V 5.97 Å, Cryo-EM structure of 5-subunit Smc5/6 arm region
8I4W 6.01 Å, Cryo-EM structure of 5-subunit Smc5/6 head region
8I21 6.02 Å, Cryo-EM structure of 6-subunit Smc5/6 arm region
8WJO 6.04 Å, Cryo-EM structure of 8-subunit Smc5/6 arm region
8WJL 6.15 Å, Cryo-EM structure of 6-subunit Smc5/6 hinge region
7YLM 6.17 Å, Cryo-EM structure of 8-subunit Smc5/6 hinge region
8I4U 6.73 Å, Cryo-EM structure of 5-subunit Smc5/6 hinge region

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