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- EMDB-4031: An engineered trimeric human cohesin complex (-SA1) bound to Pds5B -

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Basic information

Entry
Database: EMDB / ID: EMD-4031
TitleAn engineered trimeric human cohesin complex (-SA1) bound to Pds5B
Map data
Sample
  • Complex: Trimeric bonsai cohesin complex (-SA1) bound to Pds5B
    • Protein or peptide: SMC1_truncated
    • Protein or peptide: SMC3_truncated
    • Protein or peptide: SCC1
    • Protein or peptide: PDS5B
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 35.0 Å
AuthorsHons MT / Huis in't Veld PJ / Stark H / Peters J-M
CitationJournal: Nat Commun / Year: 2016
Title: Topology and structure of an engineered human cohesin complex bound to Pds5B.
Authors: Michael T Hons / Pim J Huis In 't Veld / Jan Kaesler / Pascaline Rombaut / Alexander Schleiffer / Franz Herzog / Holger Stark / Jan-Michael Peters /
Abstract: The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated ...The cohesin subunits Smc1, Smc3 and Scc1 form large tripartite rings which mediate sister chromatid cohesion and chromatin structure. These are thought to entrap DNA with the help of the associated proteins SA1/2 and Pds5A/B. Structural information is available for parts of cohesin, but analyses of entire cohesin complexes are limited by their flexibility. Here we generated a more rigid 'bonsai' cohesin by truncating the coiled coils of Smc1 and Smc3 and used single-particle electron microscopy, chemical crosslinking-mass spectrometry and in silico modelling to generate three-dimensional models of cohesin bound to Pds5B. The HEAT-repeat protein Pds5B forms a curved structure around the nucleotide-binding domains of Smc1 and Smc3 and bridges the Smc3-Scc1 and SA1-Scc1 interfaces. These results indicate that Pds5B forms an integral part of the cohesin ring by contacting all other cohesin subunits, a property that may reflect the complex role of Pds5 proteins in controlling cohesin-DNA interactions.
History
DepositionJun 15, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0141
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0141
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4031.png

Downloads & links

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Map

FileDownload / File: emd_4031.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.51 Å/pix.
x 180 pix.
= 451.8 Å		2.51 Å/pix.
x 180 pix.
= 451.8 Å		2.51 Å/pix.
x 180 pix.
= 451.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0141 / Movie #1: 0.0141
Minimum - Maximum-0.020334322 - 0.08870078
Average (Standard dev.)0.00020736722 (±0.0030226244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 451.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.512.512.51
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z451.800451.800451.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0200.0890.000

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Supplemental data

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Sample components

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Entire : Trimeric bonsai cohesin complex (-SA1) bound to Pds5B

EntireName: Trimeric bonsai cohesin complex (-SA1) bound to Pds5B
Components
  • Complex: Trimeric bonsai cohesin complex (-SA1) bound to Pds5B
    • Protein or peptide: SMC1_truncated
    • Protein or peptide: SMC3_truncated
    • Protein or peptide: SCC1
    • Protein or peptide: PDS5B

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Supramolecule #1: Trimeric bonsai cohesin complex (-SA1) bound to Pds5B

SupramoleculeName: Trimeric bonsai cohesin complex (-SA1) bound to Pds5B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 / Recombinant plasmid: pFL (multiBac) - derived
Molecular weightTheoretical: 529 KDa

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Macromolecule #1: SMC1_truncated

MacromoleculeName: SMC1_truncated / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGAE DRTFARVIVG GSSEYKINNK VVQLHEYSEE LEKLGILIKA RNFLVFQGAV ESIAMKNPKE RTALFEEISR SGELAQEYDK ...String:
MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGAE DRTFARVIVG GSSEYKINNK VVQLHEYSEE LEKLGILIKA RNFLVFQGAV ESIAMKNPKE RTALFEEISR SGELAQEYDK RKKEMVKAEE DTQFNYHRKK NIAAERKEAK PGRKAEIMES IKRLYPGSVY GRLIDLCQPT QKKYQIAVTK VLGKNMDAII VDSEKTGRDC IQYIKEQRGE PETFLPLDYL EVKPTDEKLR ELKGAKLVID VIRYEPPHIK KALQYACGNA LVCDNVEDAR RIAFGGHQRH KTVALDGTLF QKSGVISGGA SDLKAKARRW DEKAVDKLKS RLIEIDYGDL CEDLKDAQAE EEIKQEMNTL QQKLNEQQSV LQRIAAPNMK AMEKLESVRD KFQETSDEFE AARKRAKKAK QAFEQIKKER FDRFNACFES VATNIDEIYK ALSRNSSAQA FLGPENPEEP YLDGINYNCV APGKRFRPMD NLSGGEKTVA ALALLFAIHS YKPAPFFVLD EIDAALDNTN IGKVANYIKE QSTCNFQAIV ISLKEEFYTK AESLIGVYPE QGDCVISKVL TFDLTKYPDA NPNPNEQ

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Macromolecule #2: SMC3_truncated

MacromoleculeName: SMC3_truncated / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYIKQVIIQG FRSYRDQTIV DPFSSKHNVI VGRNGSGKSN FFYAIQFVLS DEFSHLRPEQ RLALLHEGTG PRVISAFVEI IFDNSDNRLP IDKEEVSLRR VIGAKKDQYF LDKKMVTKND VMNLLESAGF SRSNPYYIVK QGKINQMATA PDSQRLKLLR EVAGTRVYDE ...String:
MYIKQVIIQG FRSYRDQTIV DPFSSKHNVI VGRNGSGKSN FFYAIQFVLS DEFSHLRPEQ RLALLHEGTG PRVISAFVEI IFDNSDNRLP IDKEEVSLRR VIGAKKDQYF LDKKMVTKND VMNLLESAGF SRSNPYYIVK QGKINQMATA PDSQRLKLLR EVAGTRVYDE RKEESISLMK ETEGKREKIN ELLKYIEERL HTLEGTKKQQ LLRAATGKAI LNGIDSINKV LDHFRRKGIN QHVQNGYHGI VMNNFECEPA FYTCVEVTAG NRLFYHIVDS DEVSTKILME FNKMNLPGEV TFLPLNKLDV RDTAYPETND AIPMISKLRY NPRFDKAFKH VFGKTLICRS MEVSTQLARA FTMDCITLEG DQVSHRGALT GGYYDTRKSR LELQKDVRKA ARYQTLSLKQ LFRKLEQCNT ELKKYSHVNK KALDQFVNFS EQKEKLIKRQ EELDRGYKSI MELMNVLELR KYEAIQLTFK QVSKNFSEVF QKLVPGGKAT LVMKKGDVEG SQSQDEGEGS GESERGSGSQ SSVPSVDQFT GVGIRVSFTG KQGEMREMQQ LSGGQKSLVA LALIFAIQKC DPAPFYLFDE IDQALDAQHR KAVSDMIMEL AVHAQFITTT FRPELLESAD KFYGVKFRNK VSHIDVITAE MAKDFVEDDT THGDYKDDDD K

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Macromolecule #3: SCC1

MacromoleculeName: SCC1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFYAHFVLSK RGPLAKIWLA AHWDKKLTKA HVFECNLESS VESIISPKVK MALRTSGHLL LGVVRIYHRK AKYLLADCNE AFIKIKMAFR PGVVDLPEEN REAAYNAITL PEEFHDFDQP LPDLDDIDVA QQFSLNQSRV EEITMREEVG NISILQENDF GDFGMDDREI ...String:
MFYAHFVLSK RGPLAKIWLA AHWDKKLTKA HVFECNLESS VESIISPKVK MALRTSGHLL LGVVRIYHRK AKYLLADCNE AFIKIKMAFR PGVVDLPEEN REAAYNAITL PEEFHDFDQP LPDLDDIDVA QQFSLNQSRV EEITMREEVG NISILQENDF GDFGMDDREI MREGSAFEDD DMLVSTTTSN LLLESEQSTS NLNEKINHLE YEDQYKDDNF GEGNDGGILD DKLISNNDGG IFDDPPALSE AGVMLPEQPA HDDMDEDDNV SMGGPDSPDS VDPVEPMPTM TDQTTLVPNE EEAFALEPID ITVKETKAKR KRKLIVDSVK ELDSKTIRAQ LSDYSDIVTT LDLAPPTKKL MMWKETGGVE KLFSLPAQPL WNNRLLKLFT RCLTPLVPED LRKRRKGGEA DNLDEFLKEF ENPEVPREDQ QQQHQQRDVI DEPIIEEPSR LQESVMEASR TNIDESAMPP PPPQGVKRKA GQIDPEPVMP PQQVEQMEIP PVELPPEEPP NICQLIPELE LLPEKEKEKE KEKEDDEEEE DEDASGGDQD QEERRWNKRT QQMLHGLQRA LAKTGAESIS LLELCRNTNR KQAAAKFYSF LVLKKQQAIE LTQEEPYSDI IATPGPRFHI I

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Macromolecule #4: PDS5B

MacromoleculeName: PDS5B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HAGGAAHSKT RTNDGKITYP PGVKEISDKI SKEEMVRRLK MVVKTFMDMD QDSEEEKELY LNLALHLASD FFLKHPDKDV RLLVACCLAD IFRIYAPEAP YTSPDKLKDI FMFITRQLKG LEDTKSPQFN RYFYLLENIA WVKSYNICFE LEDSNEIFTQ ...String:
MHHHHHHHHH HAGGAAHSKT RTNDGKITYP PGVKEISDKI SKEEMVRRLK MVVKTFMDMD QDSEEEKELY LNLALHLASD FFLKHPDKDV RLLVACCLAD IFRIYAPEAP YTSPDKLKDI FMFITRQLKG LEDTKSPQFN RYFYLLENIA WVKSYNICFE LEDSNEIFTQ LYRTLFSVIN NGHNQKVHMH MVDLMSSIIC EGDTVSQELL DTVLVNLVPA HKNLNKQAYD LAKALLKRTA QAIEPYITNF FNQVLMLGKT SISDLSEHVF DLILELYNID SHLLLSVLPQ LEFKLKSNDN EERLQVVKLL AKMFGAKDSE LASQNKPLWQ CYLGRFNDIH VPIRLECVKF ASHCLMNHPD LAKDLTEYLK VRSHDPEEAI RHDVIVSIVT AAKKDILLVN DHLLNFVRER TLDKRWRVRK EAMMGLAQIY KKYALQSAAG KDAAKQIAWI KDKLLHIYYQ NSIDDRLLVE RIFAQYMVPH NLETTERMKC LYYLYATLDL NAVKALNEMW KCQNLLRHQV KDLLDLIKQP KTDASVKAIF SKVMVITRNL PDPGKAQDFM KKFTQVLEDD EKIRKQLEVL VSPTCSCKQA EGCVREITKK LGNPKQPTNP FLEMIKFLLE RIAPVHIDTE SISALIKQVN KSIDGTADDE DEGVPTDQAI RAGLELLKVL SFTHPISFHS AETFESLLAC LKMDDEKVAE AALQIFKNTG SKIEEDFPHI RSALLPVLHH KSKKGPPRQA KYAIHCIHAI FSSKETQFAQ IFEPLHKSLD PSNLEHLITP LVTIGHIALL APDQFAAPLK SLVATFIVKD LLMNDRLPGK KTTKLWVPDE EVSPETMVKI QAIKMMVRWL LGMKNNHSKS GTSTLRLLTT ILHSDGDLTE QGKISKPDMS RLRLAAGSAI VKLAQEPCYH EIITLEQYQL CALAINDECY QVRQVFAQKL HKGLSRLRLP LEYMAICALC AKDPVKERRA HARQCLVKNI NVRREYLKQH AAVSEKLLSL LPEYVVPYTI HLLAHDPDYV KVQDIEQLKD VKECLWFVLE ILMAKNENNS HAFIRKMVEN IKQTKDAQGP DDAKMNEKLY TVCDVAMNII MSKSTTYSLE SPKDPVLPAR FFTQPDKNFS NTKNYLPPEM KSFFTPGKPK TTNVLGAVNK PLSSAGKQSQ TKSSRMETVS NASSSSNPSS PGRIKGRLDS SEMDHSENED YTMSSPLPGK KSDKRDDSDL VRSELEKPRG RKKTPVTEQE EKLGMDDLTK LVQEQKPKGS QRSRKRGHTA SESDEQQWPE EKRLKEDILE NEDEQNSPPK KGKRGRPPKP LGGGTPKEEP TMKTSKKGSK KKSGPPAPEE EEEEERQSGN TEQKSKSKQH RVSRRAQQRA ESPESSAIES TQSTPQKGRG RPSKTPSPSQ PKKNVRVGRS KQAATKENDS SEEVDVFQGS SPVDDIPQEE TEEEEVSTVN VRRRSAKRER R

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHepes pH 7.5
150.0 mMNaCl
2.0 mMMgCl2
0.183 mMATPgammaS

Details: Continuous 15-40% (v/v) glycerol gradients with a 10% glycerol cushion (0.1 mL): 25 mM Hepes pH 7.5, 150 mM NaCl, 2mM MgCl2 0.183 mM ATPgammaS stabilization was accomplished by a modified ...Details: Continuous 15-40% (v/v) glycerol gradients with a 10% glycerol cushion (0.1 mL): 25 mM Hepes pH 7.5, 150 mM NaCl, 2mM MgCl2 0.183 mM ATPgammaS stabilization was accomplished by a modified GraFix protocol: 0.1% (v/v) glutaraldehyde in the 40% glycerol fraction 1 mM N-(p-Maleimidophenyl)isocyanate (PMPI) in DMSO in the 15% glycerol fraction
StainingType: NEGATIVE / Material: Uranyl Formate
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 82472
Final reconstructionResolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 3997
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 2 / Avg.num./class: 3883
Software - details: Relion 1.3 was used for 3D classification

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