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- EMDB-4571: Elongator catalytic subcomplex Elp123 lobe -

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Basic information

Entry
Database: EMDB / ID: EMD-4571
TitleElongator catalytic subcomplex Elp123 lobe
Map dataPostprocessed map of Elongator catalytic subcomplex Elp123 lobe from yeast at 3.3 A resolution.
Sample
  • Complex: Elongator catalytic subcomplex Elp123
    • Protein or peptide: Elongator complex protein 1
    • Protein or peptide: Elongator complex protein 2
    • Protein or peptide: Elongator complex protein 3
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 5'-DEOXYADENOSINE
KeywordsElongator / yeast / tRNA modification / Elp123 / TRANSLATION
Function / homology
Function and homology information


tRNA uridine(34) acetyltransferase activity / tRNA carboxymethyluridine synthase / elongator holoenzyme complex / protein urmylation / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / protein transport / regulation of translation / 4 iron, 4 sulfur cluster binding / microtubule binding ...tRNA uridine(34) acetyltransferase activity / tRNA carboxymethyluridine synthase / elongator holoenzyme complex / protein urmylation / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / protein transport / regulation of translation / 4 iron, 4 sulfur cluster binding / microtubule binding / tRNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Elongator complex protein 1 / Elongator complex protein 2 / IKI3 family / Radical SAM, C-terminal extension / Elongator complex protein 3-like / ELP3/YhcC / Radical_SAM C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily ...Elongator complex protein 1 / Elongator complex protein 2 / IKI3 family / Radical SAM, C-terminal extension / Elongator complex protein 3-like / ELP3/YhcC / Radical_SAM C-terminal domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Elongator complex protein 2 / Elongator complex protein 3 / Elongator complex protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDauden MI / Weis F
Funding support Germany, Poland, 2 items
OrganizationGrant numberCountry
German Research FoundationBR921/9-1 & Mu3173/2-1 Germany
Polish National Science CentreUMO-2015/19/B/NZ1/00343 Poland
CitationJournal: Sci Adv / Year: 2019
Title: Molecular basis of tRNA recognition by the Elongator complex.
Authors: Maria I Dauden / Marcin Jaciuk / Felix Weis / Ting-Yu Lin / Carolin Kleindienst / Nour El Hana Abbassi / Heena Khatter / Rościsław Krutyhołowa / Karin D Breunig / Jan Kosinski / Christoph ...Authors: Maria I Dauden / Marcin Jaciuk / Felix Weis / Ting-Yu Lin / Carolin Kleindienst / Nour El Hana Abbassi / Heena Khatter / Rościsław Krutyhołowa / Karin D Breunig / Jan Kosinski / Christoph W Müller / Sebastian Glatt /
Abstract: The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of ...The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer.
History
DepositionJan 28, 2019-
Header (metadata) releaseFeb 6, 2019-
Map releaseJul 17, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qk7
  • Surface level: 0.0452
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4571.png

Downloads & links

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Map

FileDownload / File: emd_4571.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of Elongator catalytic subcomplex Elp123 lobe from yeast at 3.3 A resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 290 pix.
= 391.5 Å		1.35 Å/pix.
x 290 pix.
= 391.5 Å		1.35 Å/pix.
x 290 pix.
= 391.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0452 / Movie #1: 0.0452
Minimum - Maximum-0.109405376 - 0.4307079
Average (Standard dev.)0.00040084976 (±0.00539636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 391.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z391.500391.500391.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290290
D min/max/mean-0.1090.4310.000

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Supplemental data

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Additional map: LocScale map of Elongator catalytic subcomplex Elp123 lobe...

Fileemd_4571_additional_1.map
AnnotationLocScale map of Elongator catalytic subcomplex Elp123 lobe including the dimerization domain (DD) of Elp1, used to build the atomic model of the C-terminal domains of Elp1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LocScale map of Elongator catalytic subcomplex Elp123 lobe...

Fileemd_4571_additional_2.map
AnnotationLocScale map of Elongator catalytic subcomplex Elp123 lobe used to build the atomic model.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Elongator catalytic subcomplex Elp123 lobe from yeast.

Fileemd_4571_half_map_1.map
AnnotationHalf map of Elongator catalytic subcomplex Elp123 lobe from yeast.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Elongator catalytic subcomplex Elp123 lobe from yeast.

Fileemd_4571_half_map_2.map
AnnotationHalf map of Elongator catalytic subcomplex Elp123 lobe from yeast.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Elongator catalytic subcomplex Elp123

EntireName: Elongator catalytic subcomplex Elp123
Components
  • Complex: Elongator catalytic subcomplex Elp123
    • Protein or peptide: Elongator complex protein 1
    • Protein or peptide: Elongator complex protein 2
    • Protein or peptide: Elongator complex protein 3
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 5'-DEOXYADENOSINE

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Supramolecule #1: Elongator catalytic subcomplex Elp123

SupramoleculeName: Elongator catalytic subcomplex Elp123 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The EM map corresponds to one lobe of the Elp123 complex, that includes one copy of Elp1, Elp2 and Elp3, and the C-terminal part of a second copy of Elp1.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 621 KDa

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Macromolecule #1: Elongator complex protein 1

MacromoleculeName: Elongator complex protein 1 / type: protein_or_peptide / ID: 1
Details: Chain D corresponds to the C-terminal domain of Elp1
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 153.166266 KDa
SequenceString: MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIGA IEVQQFMKDG SRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII TATYDPVSLD PAETLIEIMG TIDNGIAAAQ WSYDEETLAM V TKDRNVVV ...String:
MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIGA IEVQQFMKDG SRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII TATYDPVSLD PAETLIEIMG TIDNGIAAAQ WSYDEETLAM V TKDRNVVV LSKLFEPISE YHLEVDDLKI SKHVTVGWGK KETQFRGKGA RAMEREALAS LKASGLVGNQ LRDPTMPYMV DT GDVTALD SHEITISWRG DCDYFAVSSV EEVPDEDDET KSIKRRAFRV FSREGQLDSA SEPVTGMEHQ LSWKPQGSLI ASI QRKTDL GEEDSVDVIF FERNGLRHGE FDTRLPLDEK VESVCWNSNS EALAVVLANR IQLWTSKNYH WYLKQELYAS DISY VKWHP EKDFTLMFSD AGFINIVDFA YKMAQGPTLE PFDNGTSLVV DGRTVNITPL ALANVPPPMY YRDFETPGNV LDVAC SFSN EIYAAINKDV LIFAAVPSIE EMKKGKHPSI VCEFPKSEFT SEVDSLRQVA FINDSIVGVL LDTDNLSRIA LLDIQD ITQ PTLITIVEVY DKIVLLRSDF DYNHLVYETR DGTVCQLDAE GQLMEITKFP QLVRDFRVKR VHNTSAEDDD NWSAESS EL VAFGITNNGK LFANQVLLAS AVTSLEITDS FLLFTTAQHN LQFVHLNSTD FKPLPLVEEG VEDERVRAIE RGSILVSV I PSKSSVVLQA TRGNLETIYP RIMVLAEVRK NIMAKRYKEA FIVCRTHRIN LDILHDYAPE LFIENLEVFI NQIGRVDYL NLFISCLSED DVTKTKYKET LYSGISKSFG MEPAPLTEMQ IYMKKKMFDP KTSKVNKICD AVLNVLLSNP EYKKKYLQTI ITAYASQNP QNLSAALKLI SELENSEEKD SCVTYLCFLQ DVNVVYKSAL SLYDVSLALL VAQKSQMDPR EYLPFLQELQ D NEPLRRKF LIDDYLGNYE KALEHLSEID KDGNVSEEVI DYVESHDLYK HGLALYRYDS EKQNVIYNIY AKHLSSNQMY TD AAVAYEM LGKLKEAMGA YQSAKRWREA MSIAVQKFPE EVESVAEELI SSLTFEHRYV DAADIQLEYL DNVKEAVALY CKA YRYDIA SLVAIKAKKD ELLEEVVDPG LGEGFGIIAE LLADCKGQIN SQLRRLRELR AKKEENPYAF YGQETEQADD VSVA PSETS TQESFFTRYT GKTGGTAKTG ASRRTAKNKR REERKRARGK KGTIYEEEYL VQSVGRLIER LNQTKPDAVR VVEGL CRRN MREQAHQIQK NFVEVLDLLK ANVKEIYSIS EKDRERVNEN GEVYYIPEIP VPEIHDFPKS HIVDF

UniProtKB: Elongator complex protein 1

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Macromolecule #2: Elongator complex protein 2

MacromoleculeName: Elongator complex protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 89.51943 KDa
SequenceString: MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVPD SDFMVSASED HHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV GCADGTISIW RQNIQNDEFG LAHEFTIKKG FFYPLCLSLS K VEEKKYLL ...String:
MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVPD SDFMVSASED HHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV GCADGTISIW RQNIQNDEFG LAHEFTIKKG FFYPLCLSLS K VEEKKYLL AIGGTNVNVF IASFILSDSG IEKCRVVAEL EGHEDWVKSL AFRHQETPGD YLLCSGSQDR YIRLWRIRIN DL IDDSEED SKKLTLLSNK QYKFQIDDEL RVGINFEALI MGHDDWISSL QWHESRLQLL AATADTSLMV WEPDETSGIW VCS LRLGEM SSKGASTATG SSGGFWSCLW FTHERMDFFL TNGKTGSWRM WATKDNIICD QRLGISGATK DVTDIAWSPS GEYL LATSL DQTTRLFAPW IYDASGRKRE IATWHEFSRP QIHGYDMICV ETVTDTRFVS GGDEKILRSF DLPKGVAGML QKFVG IQFE EKSEMPDSAT VPVLGLSNKA GEDDANEDDE EEEGGNKETP DITDPLSLLE CPPMEDQLQR HLLWPEVEKL YGHGFE ITC LDISPDQKLI ASACRSNNVQ NAVIRIFSTE NWLEIKPALP FHSLTITRLK FSKDGKFLLS VCRDRKWALW ERNMEDN TF ELRFKNEKPH TRIIWDADWA PLEFGNVFVT ASRDKTVKVW RHQKEPADDY VLEASIKHTK AVTAISIHDS MIREKILI S VGLENGEIYL YSYTLGKFEL ITQLNEDITP ADKITRLRWS HLKRNGKLFL GVGSSDLSTR IYSLAYE

UniProtKB: Elongator complex protein 2

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Macromolecule #3: Elongator complex protein 3

MacromoleculeName: Elongator complex protein 3 / type: protein_or_peptide / ID: 3 / Details: FeS cluster and 5DA / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 63.755059 KDa
SequenceString: MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDII NSIPDQYKKY LLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV YCPGGPDSDF EYSTQSYTGY EPTSMRAIRA RYDPYEQARG R VEQLKQLG ...String:
MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDII NSIPDQYKKY LLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV YCPGGPDSDF EYSTQSYTGY EPTSMRAIRA RYDPYEQARG R VEQLKQLG HSIDKVEYVL MGGTFMSLPK EYREDFIVKL HNALSGFNGN DIDEAILYSQ QSLTKCVGIT IETRPDYCTQ TH LDDMLKY GCTRLEIGVQ SLYEDVARDT NRGHTVRSVC ETFAVSKDAG YKVVSHMMPD LPNVGMERDI EQFKEYFENP DFR TDGLKI YPTLVIRGTG LYELWKTGRY KSYSANALVD LVARILALVP PWTRIYRVQR DIPMPLVTSG VDNGNLRELA LARM KDLGT TCRDVRTREV GIQEVHHKVQ PDQVELIRRD YYANGGWETF LSYEDPKKDI LIGLLRLRKA SKKYTYRKEF TSQRT SIVR ELHVYGSVVP LHSRDPRKFQ HQGFGTLLME EAERIAKEEH GSEKISVISG VGVRNYYGKL GYELDGPYMS KRI

UniProtKB: Elongator complex protein 3

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: 5'-DEOXYADENOSINE

MacromoleculeName: 5'-DEOXYADENOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: 5AD
Molecular weightTheoretical: 251.242 Da
Chemical component information

ChemComp-5AD:
5'-DEOXYADENOSINE

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMHepesHepes
125.0 mMNaClSodium chloride
50.0 mMNaFSodium fluoride
0.1 mMNa3VO4Sodium vanadate
5.0 mMC2H6OSbeta-mercaptoethanol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: Pelco EasyGlow glow discharger, 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 2.5 ul of sample, blotting parameters: wait time 15 s, blot force 5, blot time 5-8 s..
DetailsThe sample was cross-linked with 0.01% glutaraldehyde, quenched and then plunged.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsGatan Quantum energy filter and a K2 Summit direct detector
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4614 / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe detector was operated in super resolution mode.
Particle selectionNumber selected: 1000000
Details: Initially 8563 particles were manually selected using EMAN2 boxer swarm tool, and used as 2D templates for the autopicking procedure in relion, that yielded 1 million particles.
Startup modelType of model: EMDB MAP
EMDB ID:

4151


Details: The initial model was low pass filtered to 60 A.
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 84135
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 39000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5m2n

chain_id: B, source_name: PDB, initial_model_type: experimental model

5cqs

chain_id: A, residue_range: 932-1349, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6qk7:
Elongator catalytic subcomplex Elp123 lobe

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Atomic model buiding 2

Initial modelPDB ID:

5cqs


Chain - Chain ID: D / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6qk7:
Elongator catalytic subcomplex Elp123 lobe

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