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- EMDB-35187: Cryo-EM structure of 5-subunit Smc5/6 -

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Basic information

Entry
Database: EMDB / ID: EMD-35187
TitleCryo-EM structure of 5-subunit Smc5/6
Map data
Sample
  • Complex: Cryo-EM structure of 5-subunit Smc5/6
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: E3 SUMO-protein ligase MMS21
    • Protein or peptide: Nse6
    • Protein or peptide: Non-structural maintenance of chromosome element 5
KeywordsCELL CYCLE
Function / homology
Function and homology information


Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / nuclear envelope / site of double-strand break / single-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / DNA repair / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6 / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Structural maintenance of chromosomes protein 5 / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal ...DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6 / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Structural maintenance of chromosomes protein 5 / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 SUMO-protein ligase MMS21 / DNA repair protein KRE29 / Non-structural maintenance of chromosome element 5 / Structural maintenance of chromosomes protein 5 / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsQian L / Jun Z / Xiang Z / Zhaoning W / Tong C / Duo J / Zhenguo C / Wang LF
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms.
Authors: Qian L / Jun Z / Xiang Z / Wang Z / Tong C / Duo J / Zhenguo C / Wang L
History
DepositionJan 21, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35187.png

Downloads & links

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Map

FileDownload / File: emd_35187.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 320 pix.
= 680.96 Å		2.13 Å/pix.
x 320 pix.
= 680.96 Å		2.13 Å/pix.
x 320 pix.
= 680.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum0.0 - 8.981365
Average (Standard dev.)0.0013054496 (±0.03735823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 680.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of 5-subunit Smc5/6

EntireName: Cryo-EM structure of 5-subunit Smc5/6
Components
  • Complex: Cryo-EM structure of 5-subunit Smc5/6
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: E3 SUMO-protein ligase MMS21
    • Protein or peptide: Nse6
    • Protein or peptide: Non-structural maintenance of chromosome element 5

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Supramolecule #1: Cryo-EM structure of 5-subunit Smc5/6

SupramoleculeName: Cryo-EM structure of 5-subunit Smc5/6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288C

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Macromolecule #1: Structural maintenance of chromosomes protein 5

MacromoleculeName: Structural maintenance of chromosomes protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 123.390031 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KRVKIAKPDL SSFQPGSIIK IRLQDFVTYT LTEFNLSPSL NMIIGPNGSG KSTFVCAVCL GLAGKPEYIG RSKKVEDFIK NGQDVSKIE ITLKNSPNVT DIEYIDARDE TIKITRIITR SKRRSDYLIN DYQVSESVVK TLVAQLNIQL DNLCQFLSQE R VEEFARLK ...String:
KRVKIAKPDL SSFQPGSIIK IRLQDFVTYT LTEFNLSPSL NMIIGPNGSG KSTFVCAVCL GLAGKPEYIG RSKKVEDFIK NGQDVSKIE ITLKNSPNVT DIEYIDARDE TIKITRIITR SKRRSDYLIN DYQVSESVVK TLVAQLNIQL DNLCQFLSQE R VEEFARLK SVKLLVETIR SIDASLLDVL DELRELQGNE QSLQKDLDFK KAKIVHLRQE SDKLRKSVES LRDFQNKKGE IE LHSQLLP YVKVKDHKEK LNIYKEEYER AKANLRAILK DKKPFANTKK TLENQVEELT EKCSLKTDEF LKAKEKINEI FEK LNTIRD EVIKKKNQNE YYRGRTKKLQ ATIISTKEDF LRSQEILAQT HLPEKSVFED IDIKRKEIIN KEGEIRDLIS EIDA KANAI NHEMRSIQRQ AESKTKSLTT TDKIGILNQD QDLKEVRDAV LMVREHPEMK DKILEPPIMT VSAINAQFAA YLAQC VDYN TSKALTVVDS DSYKLFANPI LDKFKVNLRE LSSADTTPPV PAETVRDLGF EGYLSDFITG DKRVMKMLCQ TSKIHT IPV SRRELTPAQI KKLITPRPNG KILFKRIIHG NRLVDIKQSA YGSKQVFPTD VSIKQTNFYQ GSIMSNEQKI RIENEII NL KNEYNDRKST LDALSNQKSG YRHELSELAS KNDDINREAH QLNEIRKKYT MRKSTIETLR EKLDQLKREA RKDVSQKI K DIDDQIQQLL LKQRHLLSKM ASSMKSLKNC QKELISTQIL QFEAQNMDVS MNDVIGFFNE READLKSQYE DKKKFVKEA RDTPEFQSWM REIRSYDQDT KEKLNKVAEK YEEEGNFNLS FVQDVLDKLE SEIAMVNHDE SAVTILDQVT AELRELEHTV PQQSKDLET IKAKLKEDHA VLEPKLDDIV SKISARFARL FNNVGSAGAV RLEKPKDYAE WKIEIMVKFR DNAPLKKLDS H TQSGGERA VSTVLYMIAL QEFTSAPFRV VDEINQGMDS RNERIVHKAM VENACAENTS QYFLITPKLL TGLHYHEKMR IH CVMAGSW IPNPSEDPKM IHFGETSNYS FD

UniProtKB: Structural maintenance of chromosomes protein 5

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Macromolecule #2: Structural maintenance of chromosomes protein 6

MacromoleculeName: Structural maintenance of chromosomes protein 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 126.889375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MISTTISGKR PIEQVDDELL SLTAQQENEE QQQQRKRRRH QFAPMTQFNS NTLDEDSGFR SSSDVATADQ DNFLEESPSG YIKKVILRN FMCHEHFELE LGSRLNFIVG NNGSGKSAIL TAITIGLGAK ASETNRGSSL KDLIREGCYS AKIILHLDNS K YGAYQQGI ...String:
MISTTISGKR PIEQVDDELL SLTAQQENEE QQQQRKRRRH QFAPMTQFNS NTLDEDSGFR SSSDVATADQ DNFLEESPSG YIKKVILRN FMCHEHFELE LGSRLNFIVG NNGSGKSAIL TAITIGLGAK ASETNRGSSL KDLIREGCYS AKIILHLDNS K YGAYQQGI FGNEIIVERI IKRDGPASFS LRSENGKEIS NKKKDIQTVV DYFSVPVSNP MCFLSQDAAR SFLTASTSQD KY SHFMKGT LLQEITENLL YASAIHDSAQ ENMALHLENL KSLKAEYEDA KKLLRELNQT SDLNERKMLL QAKSLWIDVA HNT DACKNL ENEISGIQQK VDEVTEKIRN RQEKIERYTS DGTTIEAQID AKVIYVNEKD SEHQNARELL RDVKSRFEKE KSNQ AEAQS NIDQGRKKVD ALNKTIAHLE EELTKEMGGD KDQMRQELEQ LEKANEKLRE VNNSLVVSAQ DVKNEERDIQ HERES ELRT ISRSIQNKKV ELQNIAKGND TFLMNFDRNM DRLLRTIEQR KNEFETPAIG PLGSLVTIRK GFEKWTRSIQ RAISSS LNA FVVSNPKDNR LFRDIMRSCG IRSNIPIVTY CLSQFDYSKG RAHGNYPTIV DALEFSKPEI ECLFVDLSRI ERIVLIE DK NEARNFLQRN PVNVNMALSL RDRRSGFQLS GGYRLDTVTY QDKIRLKVNS SSDNGTQYLK DLIEQETKEL QNIRDRYE E KLSEVRSRLK EIDGRLKSTK NEMRKTNFRM TELKMNVGKV VDTGILNSKI NERKNQEQAI ASYEAAKEEL GLKIEQIAQ EAQPIKEQYD STKLALVEAQ DELQQLKEDI NSRQSKIQKY KDDTIYYEDK KKVYLENIKK IEVNVAALKE GIQRQIQNAC AFCSKERIE NVDLPDTQEE IKRELDKVSR MIQKAEKSLG LSQEEVIALF EKCRNKYKEG QKKYMEIDEA LNRLHNSLKA R DQNYKNAE KGTCFDADMD FRASLKVRKF SGNLSFIKDT KSLEIYILTT NDEKARNVDT LSGGEKSFSQ MALLLATWKP MR SRIIALD EFDVFMDQVN RKIGTTLIVK KLKDIARTQT IIITPQDIGK IADIDSSGVS IHRMRDP

UniProtKB: Structural maintenance of chromosomes protein 6

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Macromolecule #3: E3 SUMO-protein ligase MMS21

MacromoleculeName: E3 SUMO-protein ligase MMS21 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 30.388336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALNDNPIPK SVPLHPKSGK YFHNLHARDL SNIYQQCYKQ IDETINQLVD STSPSTIGIE EQVADITSTY KLLSTYESES NSFDEHIKD LKKNFKQSSD ACPQIDLSTW DKYRTGELTA PKLSELYLNM PTPEPATMVN NTDTLKILKV LPYIWNDPTC V IPDLQNPA ...String:
MALNDNPIPK SVPLHPKSGK YFHNLHARDL SNIYQQCYKQ IDETINQLVD STSPSTIGIE EQVADITSTY KLLSTYESES NSFDEHIKD LKKNFKQSSD ACPQIDLSTW DKYRTGELTA PKLSELYLNM PTPEPATMVN NTDTLKILKV LPYIWNDPTC V IPDLQNPA DEDDLQIEGG KIELTCPITC KPYEAPLISR KCNHVFDRDG IQNYLQGYTT RDCPQAACSQ VVSMRDFVRD PI MELRCKI AKMKESQEQD KRSSQAIDVL

UniProtKB: E3 SUMO-protein ligase MMS21

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Macromolecule #4: Nse6

MacromoleculeName: Nse6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 44.498242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PILKRTIISK RKAPSNNEDE EIVKTPRKLV NYVPLKIFNL GDSFDDTITT TVAKLQDLKK EILDSPRSNK SIVITSNTVA KSELQKSIK FSGSIPEIYL DVVTKETISD KYKDWHFISK NCHYEQLMDL EMKDTAYSFL FGSSRSQGKV PEFVHLKCPS I TNLLVLFG ...String:
PILKRTIISK RKAPSNNEDE EIVKTPRKLV NYVPLKIFNL GDSFDDTITT TVAKLQDLKK EILDSPRSNK SIVITSNTVA KSELQKSIK FSGSIPEIYL DVVTKETISD KYKDWHFISK NCHYEQLMDL EMKDTAYSFL FGSSRSQGKV PEFVHLKCPS I TNLLVLFG VNQEKCNSLK INYEKKENSR YDNLCTIFPV NKMLKFLMYF YSDDDNDDVR EFFLKAFICL ILDRKVFNAM ES DHRLCFK VLELFNEAHF INSYFEIVDK NDFFLHYRLL QIFPHLQSAL LRRRFSEKQG RTETIQQNII KEFNEFFDCK NYK NLLYFI LTMYGSKFIP FGPKCQVTEY FKDCILDISN ETTNDVEISI LKGILNLFSK IR

UniProtKB: DNA repair protein KRE29

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Macromolecule #5: Non-structural maintenance of chromosome element 5

MacromoleculeName: Non-structural maintenance of chromosome element 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 64.079609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDGALINSVL YVSPRNGAHY FVELTEKHLL AFEMLNSMCL LENYDHVLLF LECQFGKSHN LAVIPFDIIL VLFTLSTLSE YYKEPILRA NDPYNTSRET LSRRALKLLQ KYLAILKEFD SEQYNLYDLE LLRCQFFLAI DTLTPKKQKW GFDRFRRTKS E SGVTYRQN ...String:
MDGALINSVL YVSPRNGAHY FVELTEKHLL AFEMLNSMCL LENYDHVLLF LECQFGKSHN LAVIPFDIIL VLFTLSTLSE YYKEPILRA NDPYNTSRET LSRRALKLLQ KYLAILKEFD SEQYNLYDLE LLRCQFFLAI DTLTPKKQKW GFDRFRRTKS E SGVTYRQN ASVDPELDQA KTFKNPYRSY ISCLEQRNTI LGNRLLNLKL NEPGEFINMI LWTLSNSLQE STPLFLSSHE IW MPLLEIL IDLFSCRQDY FIQHEVAQNV SKSLFVQRLS ESPLAVFFES LNTRNFANRF SEYVFLNCDY KLPSDNYATP VHP VYNGEN TIVDTYIPTI KCSPLYKSQK SLALRRKLIG SCFKLLLRVP DGHRLITPRI VADDVIQGIS RTLASFNDIL QFKK FFMTE NLSQESYFIP LLAEGTLSEI LKDTQECVVI LTLVENLSDG VSFCNEVIGL VKSKCFAFTE QCSQASYEEA VLNIE KCDV CLLVLLRYLL HLIGTEAILD AKEQLEMLHA IEKNDSGRRQ WAKALNLGND PPLLYPIVSQ MFGVHDKSVI IE

UniProtKB: Non-structural maintenance of chromosome element 5

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 268567
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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