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- EMDB-23570: Structure of yeast DNA Polymerase Zeta (apo) -

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Basic information

Entry
Database: EMDB / ID: EMD-23570
TitleStructure of yeast DNA Polymerase Zeta (apo)
Map datacryo-em map of apo-PolZ
Sample
  • Complex: DNA polymerase Zeta
    • Protein or peptide: DNA polymerase zeta catalytic subunit
    • Protein or peptide: DNA polymerase zeta processivity subunit
    • Protein or peptide: DNA polymerase delta small subunit
    • Protein or peptide: DNA polymerase delta subunit 3
  • Ligand: IRON/SULFUR CLUSTER
Keywordsnucleic acid binding / DNA polymerase / metal ion binding / catalytic activity / DNA BINDING PROTEIN
Function / homology
Function and homology information


delta DNA polymerase complex / H3-H4 histone complex chaperone activity / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / Translesion synthesis by REV1 / Translesion synthesis by POLK ...delta DNA polymerase complex / H3-H4 histone complex chaperone activity / DNA amplification / zeta DNA polymerase complex / RNA-templated DNA biosynthetic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / DNA replication, removal of RNA primer / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / DNA strand elongation involved in DNA replication / DNA metabolic process / error-free translesion synthesis / leading strand elongation / error-prone translesion synthesis / mismatch repair / nucleotide-excision repair / double-strand break repair via homologous recombination / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin / mitochondrion / DNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase zeta catalytic subunit / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase zeta catalytic subunit / DNA polymerase zeta processivity subunit / DNA polymerase delta small subunit / DNA polymerase delta subunit 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsTruong CD / Craig TA
CitationJournal: J Biol Chem / Year: 2021
Title: Cryo-EM reveals conformational flexibility in apo DNA polymerase ζ.
Authors: Chloe Du Truong / Theodore A Craig / Gaofeng Cui / Maria Victoria Botuyan / Rachel A Serkasevich / Ka-Yi Chan / Georges Mer / Po-Lin Chiu / Rajiv Kumar /
Abstract: The translesion synthesis (TLS) DNA polymerases Rev1 and Polζ function together in DNA lesion bypass during DNA replication, acting as nucleotide inserter and extender polymerases, respectively. ...The translesion synthesis (TLS) DNA polymerases Rev1 and Polζ function together in DNA lesion bypass during DNA replication, acting as nucleotide inserter and extender polymerases, respectively. While the structural characterization of the Saccharomyces cerevisiae Polζ in its DNA-bound state has illuminated how this enzyme synthesizes DNA, a mechanistic understanding of TLS also requires probing conformational changes associated with DNA- and Rev1 binding. Here, we used single-particle cryo-electron microscopy to determine the structure of the apo Polζ holoenzyme. We show that compared with its DNA-bound state, apo Polζ displays enhanced flexibility that correlates with concerted motions associated with expansion of the Polζ DNA-binding channel upon DNA binding. We also identified a lysine residue that obstructs the DNA-binding channel in apo Polζ, suggesting a gating mechanism. The Polζ subunit Rev7 is a hub protein that directly binds Rev1 and is a component of several other protein complexes such as the shieldin DNA double-strand break repair complex. We analyzed the molecular interactions of budding yeast Rev7 in the context of Polζ and those of human Rev7 in the context of shieldin using a crystal structure of Rev7 bound to a fragment of the shieldin-3 protein. Overall, our study provides new insights into Polζ mechanism of action and the manner in which Rev7 recognizes partner proteins.
History
DepositionMar 3, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7lxd
  • Surface level: 3.35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23570.png

Downloads & links

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Map

FileDownload / File: emd_23570.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-em map of apo-PolZ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.49 Å/pix.
x 220 pix.
= 328.02 Å		1.49 Å/pix.
x 220 pix.
= 328.02 Å		1.49 Å/pix.
x 220 pix.
= 328.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.491 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.35 / Movie #1: 3.35
Minimum - Maximum-12.993312 - 41.499836000000002
Average (Standard dev.)-0.000000000000046 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 328.02002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4911.4911.491
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z328.020328.020328.020
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-12.99341.500-0.000

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Supplemental data

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Additional map: Half-map 1

Fileemd_23570_additional_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half-map 2

Fileemd_23570_additional_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA polymerase Zeta

EntireName: DNA polymerase Zeta
Components
  • Complex: DNA polymerase Zeta
    • Protein or peptide: DNA polymerase zeta catalytic subunit
    • Protein or peptide: DNA polymerase zeta processivity subunit
    • Protein or peptide: DNA polymerase delta small subunit
    • Protein or peptide: DNA polymerase delta subunit 3
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: DNA polymerase Zeta

SupramoleculeName: DNA polymerase Zeta / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: DNA polymerase Zeta is generated from yeast without DNA binding.
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 172 kDa/nm

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Macromolecule #1: DNA polymerase zeta catalytic subunit

MacromoleculeName: DNA polymerase zeta catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 173.197531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSRESNDTIQ SDTVRSSSKS DYFRIQLNNQ DYYMSKPTFL DPSHGESLPL NQFSQVPNIR VFGALPTGHQ VLCHVHGILP YMFIKYDGQ ITDTSTLRHQ RCAQVHKTLE VKIRASFKRK KDDKHDLAGD KLGNLNFVAD VSVVKGIPFY GYHVGWNLFY K ISLLNPSC ...String:
MSRESNDTIQ SDTVRSSSKS DYFRIQLNNQ DYYMSKPTFL DPSHGESLPL NQFSQVPNIR VFGALPTGHQ VLCHVHGILP YMFIKYDGQ ITDTSTLRHQ RCAQVHKTLE VKIRASFKRK KDDKHDLAGD KLGNLNFVAD VSVVKGIPFY GYHVGWNLFY K ISLLNPSC LSRISELIRD GKIFGKKFEI YESHIPYLLQ WTADFNLFGC SWINVDRCYF RSPVLNSILD IDKLTINDDL QL LLDRFCD FKCNVLSRRD FPRVGNGLIE IDILPQFIKN REKLQHRDIH HDFLEKLGDI SDIPVKPYVS SARDMINELT MQR EELSLK EYKEPPETKR HVSGHQWQSS GEFEAFYKKA QHKTSTFDGQ IPNFENFIDK NQKFSAINTP YEALPQLWPR LPQI EINNN SMQDKKNDDQ VNASFTEYEI CGVDNENEGV KGSNIKSRSY SWLPESIASP KDSTILLDHQ TKYHNTINFS MDCAM TQNM ASKRKLRSSV SANKTSLLSR KRKKVMAAGL RYGKRAFVYG EPPFGYQDIL NKLEDEGFPK IDYKDPFFSN PVDLEN KPY AYAGKRFEIS STHVSTRIPV QFGGETVSVY NKPTFDMFSS WKYALKPPTY DAVQKWYNKV PSMGNKKTES QISMHTP HS KFLYKFASDV SGKQKRKKSS VHDSLTHLTL EIHANTRSDK IPDPAIDEVS MIIWCLEEET FPLDLDIAYE GIMIVHKA S EDSTFPTKIQ HCINEIPVMF YESEFEMFEA LTDLVLLLDP DILSGFEIHN FSWGYIIERC QKIHQFDIVR ELARVKCQI KTKLSDTWGY AHSSGIMITG RHMINIWRAL RSDVNLTQYT IESAAFNILH KRLPHFSFES LTNMWNAKKS TTELKTVLNY WLSRAQINI QLLRKQDYIA RNIEQARLIG IDFHSVYYRG SQFKVESFLI RICKSESFIL LSPGKKDVRK QKALECVPLV M EPESAFYK SPLIVLDFQS LYPSIMIGYN YCYSTMIGRV REINLTENNL GVSKFSLPRN ILALLKNDVT IAPNGVVYAK TS VRKSTLS KMLTDILDVR VMIKKTMNEI GDDNTTLKRL LNNKQLALKL LANVTYGYTS ASFSGRMPCS DLADSIVQTG RET LEKAID IIEKDETWNA KVVYGDTDSL FVYLPGKTAI EAFSIGHAMA ERVTQNNPKP IFLKFEKVYH PSILISKKRY VGFS YESPS QTLPIFDAKG IETVRRDGIP AQQKIIEKCI RLLFQTKDLS KIKKYLQNEF FKIQIGKVSA QDFCFAKEVK LGAYK SEKT APAGAVVVKR RINEDHRAEP QYKERIPYLV VKGKQGQLLR ERCVSPEEFL EGENLELDSE YYINKILIPP LDRLFN LIG INVGNWAQEI VKSKRASTTT TKVENITRVG TSATCCNCGE ELTKICSLQL CDDCLEKRST TTLSFLIKKL KRQKEYQ TL KTVCRTCSYR YTSDAGIEND HIASKCNSYD CPVFYSRVKA ERYLRDNQSV QREEALISLN DW

UniProtKB: DNA polymerase zeta catalytic subunit

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Macromolecule #2: DNA polymerase zeta processivity subunit

MacromoleculeName: DNA polymerase zeta processivity subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 28.791654 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNRWVEKWLR VYLKCYINLI LFYRNVYPPQ SFDYTTYQSF NLPQFVPINR HPALIDYIEE LILDVLSKLT HVYRFSICII NKKNDLCIE KYVLDFSELQ HVDKDDQIIT ETEVFDEFRS SLNSLIMHLE KLPKVNDDTI TFEAVINAIE LELGHKLDRN R RVDSLEEK ...String:
MNRWVEKWLR VYLKCYINLI LFYRNVYPPQ SFDYTTYQSF NLPQFVPINR HPALIDYIEE LILDVLSKLT HVYRFSICII NKKNDLCIE KYVLDFSELQ HVDKDDQIIT ETEVFDEFRS SLNSLIMHLE KLPKVNDDTI TFEAVINAIE LELGHKLDRN R RVDSLEEK AEIERDSNWV KCQEDENLPD NNGFQPPKIK LTSLVGSDVG PLIIHQFSEK LISGDDKILN GVYSQYEEGE SI FGSLF

UniProtKB: DNA polymerase zeta processivity subunit

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Macromolecule #3: DNA polymerase delta small subunit

MacromoleculeName: DNA polymerase delta small subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.603992 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: LHMDALLTKF NEDRSLQDEN LSQPRTRVRI VDDNLYNKSN PFQLCYKKRD YGSQYYHIYQ YRLKTFRERV LKECDKRWDA GFTLNGQLV LKKDKVLDIQ GNQPCWCVGS IYCEMKYKPN VLDEVINDTY GAPDLTKSYT DKEGGSDEIM LEDESGRVLL V GDFIRSTP ...String:
LHMDALLTKF NEDRSLQDEN LSQPRTRVRI VDDNLYNKSN PFQLCYKKRD YGSQYYHIYQ YRLKTFRERV LKECDKRWDA GFTLNGQLV LKKDKVLDIQ GNQPCWCVGS IYCEMKYKPN VLDEVINDTY GAPDLTKSYT DKEGGSDEIM LEDESGRVLL V GDFIRSTP FITGVVVGIL GMEAEAGTFQ VLDICYPTPL PQNPFPAPIA TCPTRGKIAL VSGLNLNNTS PDRLLRLEIL RE FLMGRIN NKIDDISLIG RLLICGNSVD FDIKSVNKDE LMISLTEFSK FLHNILPSIS VDIMPGTNDP SDKSLPQQPF HKS LFDKSL ESYFNGSNKE ILNLVTNPYE FSYNGVDVLA VSGKNINDIC KYVIPSNDNG ESENKVEEGE SNDFKDDIEH RLDL MECTM KWQNIAPTAP DTLWCYPYTD KDPFVLDKWP HVYIVANQPY FGTRVVEIGG KNIKIISVPE FSSTGMIILL DLETL EAET VKIDI

UniProtKB: DNA polymerase delta small subunit

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Macromolecule #4: DNA polymerase delta subunit 3

MacromoleculeName: DNA polymerase delta subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 40.377715 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDQKASYFIN EKLFTEVKPV LFTDLIHHLK IGPSMAKKLM FDYYKQTTNA KYNCVVICCY KDQTIKIIHD LSNIPQQDSI IDCFIYAFN PMDSFIPYYD IIDQKDCLTI KNSYELKVSE SSKIIERTKT LEEKSKPLVR PTARSKTTPE ETTGRKSKSK D MGLRSTAL ...String:
MDQKASYFIN EKLFTEVKPV LFTDLIHHLK IGPSMAKKLM FDYYKQTTNA KYNCVVICCY KDQTIKIIHD LSNIPQQDSI IDCFIYAFN PMDSFIPYYD IIDQKDCLTI KNSYELKVSE SSKIIERTKT LEEKSKPLVR PTARSKTTPE ETTGRKSKSK D MGLRSTAL LAKMKKDRDD KETSRQNELR KRKEENLQKI NKQNPEREAQ MKELNNLFVE DDLDTEEVNG GSKPNSPKET DS NDKDKNN DDLEDLLETT AEDSLMDVPK IQQTKPSETE HSKEPKSEEE PSSFIDEDGY IVTKRPATST PPRKPSPVVK RAL SSSKKQ ETPSSNKRLK KQGTLESFFK RKAK

UniProtKB: DNA polymerase delta subunit 3

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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

Concentration0.12 mg/mL
BufferpH: 6.9
Component:
ConcentrationFormulaName
25.0 mMMES2-(N-morpholino)ethanesulfonic acid
120.0 mMNaClSodium Chloride
5.0 mMCaCl2Calcium Chloride
2.0 mMTCEPtris(2-carboxyethyl)phosphine

Details: Solutions were made fresh from concentrate to avoid microbial contamination. They are further filtered using 0.2 micrometer filtering membrane and a pressure/vacuum filtration unit.
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II / Details: Blot for 6 seconds before plunging.
DetailsThis sample was mono disperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 11698 / Average exposure time: 6.0 sec. / Average electron dose: 45.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 48780 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2974553
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 213120
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0)

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Atomic model buiding 1

Initial modelPDB ID:

6v8p


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-7lxd:
Structure of yeast DNA Polymerase Zeta (apo)

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