8I4V: 5-subunit Smc5/6 arm region

Cryo-EM structure of 5-subunit Smc5/6 arm region. Determined by electron microscopy at 5.97 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 5.97 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 4
Atoms: 7,041
Mol. weight: 287.53 kDa
Released: 26 Jun 2024

Explore 8I4V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I4V contains 29 α-helices and 5 β-strands across 4 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	233-267	35
α-helix	272-363	92
α-helix	747-768	22
α-helix	771-780	10
α-helix	783-824	42
α-helix	828-832	5
α-helix	836-842	7
α-helix	847-862	16
α-helix	867-881	15
α-helix	891-903	13

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	288-400	113
α-helix	792-881	90
α-helix	897-918	22
α-helix	922-929	8

Chain C: 11 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	16-24	9
α-helix	27-29	3
α-helix	31-51	21
α-helix	60-100	41
α-helix	102-104	3
α-helix	108-114	7
α-helix	122-128	7
α-helix	130-132	3
α-helix	142-155	14
β-strand	195-197	3	1
β-strand	203-204	2	1
α-helix	209-213	5
β-strand	219-220	2	2
β-strand	229-230	2	2
β-strand	235-237	3	1
α-helix	239-253	15

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	88-93	6
α-helix	104-105	2
α-helix	110-112	3
α-helix	132-149	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 5	A	protein	1069	Saccharomyces cerevisiae S288C	Q08204 (AlphaFold model)
Structural maintenance of chromosomes protein 6	B	protein	1114	Saccharomyces cerevisiae S288C	Q12749 (AlphaFold model)
E3 SUMO-protein ligase MMS21	C	protein	251	Saccharomyces cerevisiae S288C	P38632 (AlphaFold model)
DNA repair protein KRE29	D	protein	64	Saccharomyces cerevisiae S288C	P40026 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8I4V_1 Structural maintenance of chromosomes protein 5 (chains A)
KRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNLSPSLNMIIGPNGSGKSTFVCAVCL
GLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSPNVTDIEYIDARDETIKITRIITRS
KRRSDYLINDYQVSESVVKTLVAQLNIQLDNLCQFLSQERVEEFARLKSVKLLVETIRSI
DASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLRQESDKLRKSVESLRDFQNKKGEIE
LHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAILKDKKPFANTKKTLENQVEELTEKC
SLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYRGRTKKLQATIISTKEDFLRSQ
EILAQTHLPEKSVFEDIDIKRKEIINKEGEIRDLISEIDAKANAINHEMRSIQRQAESKT
KSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKDKILEPPIMTVSAINAQFAAYLAQC
VDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELSSADTTPPVPAETVRDLGFEGYLSD
FITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKLITPRPNGKILFKRIIHGNRLVDIK
QSAYGSKQVFPTDVSIKQTNFYQGSIMSNEQKIRIENEIINLKNEYNDRKSTLDALSNQK
SGYRHELSELASKNDDINREAHQLNEIRKKYTMRKSTIETLREKLDQLKREARKDVSQKI
KDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELISTQILQFEAQNMDVSMNDVIGFFN
EREADLKSQYEDKKKFVKEARDTPEFQSWMREIRSYDQDTKEKLNKVAEKYEEEGNFNLS
FVQDVLDKLESEIAMVNHDESAVTILDQVTAELRELEHTVPQQSKDLETIKAKLKEDHAV
LEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKDYAEWKIEIMVKFRDNAPLKKLDSH
TQSGGERAVSTVLYMIALQEFTSAPFRVVDEINQGMDSRNERIVHKAMVENACAENTSQY
FLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPKMIHFGETSNYSFD

Sequence of entity 2 (B), FASTA

>8I4V_2 Structural maintenance of chromosomes protein 6 (chains B)
MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFR
SSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILT
AITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIK
RDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY
SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDL
NERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTT
IEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKT
IAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERES
ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLV
TIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDY
SKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMAL
SLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE
EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQA
IASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKY
KDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEI
KRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR
DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLS
GGEKSFSQMALLLATWKPMRSRIIALDEFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN

Sequence of entity 3 (C), FASTA

>8I4V_3 E3 SUMO-protein ligase MMS21 (chains C)
NDNPIPKSVPLHPKSGKYFHNLHARDLSNIYQQCYKQIDETINQLVDSTSPSTIGIEEQV
ADITSTYKLLSTYESESNSFDEHIKDLKKNFKQSSDACPQIDLSTWDKYRTGELTAPKLS
ELYLNMPTPEPATMVNNTDTLKILKVLPYIWNDPTCVIPDLQNPADEDDLQIEGGKIELT
CPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPIMEL
RCKIAKMKESQ

Sequence of entity 4 (D), FASTA

>8I4V_4 DNA repair protein KRE29 (chains D)
PILKRTIISKRKAPSNNEDEEIVKTPRKLVNYVPLKIFNLGDSFDDTITTTVAKLQDLKK
EILD

Primary citation

Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms. Li, Q., Zhang, J., Haluska, C. et al. Nat Struct Mol Biol (2024) 31:1532-1542. DOI 10.1038/s41594-024-01319-1 · PubMed

Other PDB entries of the same protein (UniProt Q08204 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HTK 2.31 Å, Crystal structure of Mms21 and Smc5 complex
8HQS 3.2 Å, Cryo-EM structure of 8-subunit Smc5/6 head region
7P47 3.31 Å, Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic
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
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

Browse structure collections

About this viewer

MolViewer shows 8I4V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.