EMDB-45809: The ligation complex in the NHEJ pathway

Basic information

Entry

Database: EMDB / ID: EMD-45809

• Title: The ligation complex in the NHEJ pathway
• Map data: composite map for NHEJ Ligation complex I

Sample

• Complex: Ligation complex in the NHEJ pathway
  • Protein or peptide: x 6 types
  • DNA: x 4 types
• Ligand: x 1 types

• Keywords: NHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / LIGASE-TRANSFERASE-DNA complex

Function / homology

Function:

FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA ligase (ATP) / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / immunoglobulin V(D)J recombination / nucleotide-excision repair, DNA gap filling / regulation of smooth muscle cell proliferation / single strand break repair / V(D)J recombination / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / isotype switching / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / protein localization to chromosome, telomeric region / cellular hyperosmotic salinity response / cellular response to fatty acid / positive regulation of neurogenesis / response to ionizing radiation / cellular response to lithium ion / DNA biosynthetic process / telomeric DNA binding / 2-LTR circle formation / hematopoietic stem cell proliferation / ligase activity / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / somatic stem cell population maintenance / T cell differentiation / 5'-deoxyribose-5-phosphate lyase activity / response to X-ray / ATP-dependent activity, acting on DNA / positive regulation of protein kinase activity / hematopoietic stem cell differentiation / chromosome organization / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / DNA helicase activity / condensed chromosome / DNA polymerase binding / neurogenesis / telomere maintenance / activation of innate immune response / B cell differentiation / cyclin binding / cellular response to leukemia inhibitory factor / enzyme activator activity / central nervous system development / stem cell proliferation / cellular response to ionizing radiation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / small-subunit processome / cellular response to gamma radiation / protein-DNA complex / base-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / fibrillar center / positive regulation of fibroblast proliferation / double-strand break repair / site of double-strand break / T cell differentiation in thymus / double-stranded DNA binding / scaffold protein binding / fibroblast proliferation / secretory granule lumen / neuron apoptotic process / DNA recombination / molecular adaptor activity / transcription regulator complex / negative regulation of neuron apoptotic process / in utero embryonic development / ficolin-1-rich granule lumen / damaged DNA binding / chromosome, telomeric region / cell population proliferation / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex

Domain/homology:

Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal domain superfamily / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / DNA ligase, ATP-dependent / Ku70/Ku80 C-terminal arm / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / Ku70/Ku80 C-terminal arm / DNA ligase N terminus / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / SAP domain superfamily / ATP dependent DNA ligase domain / DNA repair protein XRCC4-like, C-terminal / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily / Nucleic acid-binding, OB-fold

Component:

X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / DNA ligase 4 / DNA repair protein XRCC4 / Protein PAXX / Non-homologous end-joining factor 1

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.1 Å
• Authors: Li J / Liu L / Gellert M / Yang W

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)		United States

• Citation: Journal: Nature / Year: 2025; Title: Dynamic assemblies and coordinated reactions of non-homologous end joining.; Authors: Lan Liu / Jun Li / Metztli Cisneros-Aguirre / Arianna Merkell / Jeremy M Stark / Martin Gellert / Wei Yang / ; Abstract: Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA polymerase μ and ligase IV (LIG4) engaged in gap filling and end joining. These reactions take place in a flexible ω-shaped framework composed of XRCC4 and XLF. Two broken DNA ends, each encircled by Ku70-Ku80 internally, are docked onto the ω frame, mediated by LIG4. DNA polymerase and ligase attached to each ω arm repair only one broken strand of a defined polarity; the final steps of NHEJ requires coordination and toggling of a pair of such enzymes. The facilitators XLF and PAXX additively stimulate NHEJ reactions. As DNA-end sensor and protector, LIG4 replaces DNA-PKcs for end joining and bridges the two DNA ends for polymerase to fill remaining gaps. These assemblies present new targets for NHEJ inhibition to enhance efficacy of radiotherapy and accuracy of gene editing.

History

Deposition	Jul 19, 2024	-
Header (metadata) release	Apr 23, 2025	-
Map release	Apr 23, 2025	-
Update	Jun 25, 2025	-
Current status	Jun 25, 2025	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_45809.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: composite map for NHEJ Ligation complex I
• Voxel size: X=Y=Z: 0.833 Å

Density

Contour Level	By AUTHOR: 8.0
Minimum - Maximum	-22.344018999999999 - 73.848590000000002
Average (Standard dev.)	0.005619068 (±1.3725606)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 512 512 512 Spacing 512 512 512
Cell	A=B=C: 426.496 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_45809_msk_1.map

Additional map: Postprocessed map (by RELION) for model building and validation

• File: emd_45809_additional_1.map
• Annotation: Postprocessed map (by RELION) for model building and validation

Additional map: DeepEMhancer sharpened map for model building

• File: emd_45809_additional_2.map
• Annotation: DeepEMhancer sharpened map for model building

Half map: composite half1 map

• File: emd_45809_half_map_1.map
• Annotation: composite half1 map

Half map: composite half2 map

• File: emd_45809_half_map_2.map
• Annotation: composite half2 map

Sample components

Entire : Ligation complex in the NHEJ pathway

• Entire: Name: Ligation complex in the NHEJ pathway

Components

• Complex: Ligation complex in the NHEJ pathway
  • Protein or peptide: X-ray repair cross-complementing protein 6
  • Protein or peptide: X-ray repair cross-complementing protein 5
  • Protein or peptide: Non-homologous end-joining factor 1
  • Protein or peptide: DNA repair protein XRCC4
  • Protein or peptide: DNA ligase 4
  • Protein or peptide: Protein PAXX
  • DNA: DNA (40-MER)
  • DNA: DNA (38-MER)
  • DNA: DNA (36-MER)
  • DNA: DNA (34-MER)
• Ligand: ADENOSINE MONOPHOSPHATE

Supramolecule #1: Ligation complex in the NHEJ pathway

• Supramolecule: Name: Ligation complex in the NHEJ pathway / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 854 KDa

Macromolecule #1: X-ray repair cross-complementing protein 6

• Macromolecule: Name: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO; EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 70.198336 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPFDMSIQCI QSVYISKIIS SDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELDQFKGQQ GQKRFQDMMG HGSDYSLSEV LWVCANLFSD V QFKMSHKR IMLFTNEDNP HGNDSAKASR ARTKAGDLRD TGIFLDLMHL KKPGGFDISL FYRDIISIAE DEDLRVHFEE SS KLEDLLR KVRAKETRKR ALSRLKLKLN KDIVISVGIY NLVQKALKPP PIKLYRETNE PVKTKTRTFN TSTGGLLLPS DTK RSQIYG SRQIILEKEE TEELKRFDDP GLMLMGFKPL VLLKKHHYLR PSLFVYPEES LVIGSSTLFS ALLIKCLEKE VAAL CRYTP RRNIPPYFVA LVPQEEELDD QKIQVTPPGF QLVFLPFADD KRKMPFTEKI MATPEQVGKM KAIVEKLRFT YRSDS FENP VLQQHFRNLE ALALDLMEPE QAVDLTLPKV EAMNKRLGSL VDEFKELVYP PDYNPEGKVT KRKHDNEGSG SKRPKV EYS EEELKTHISK GTLGKFTVPM LKEACRAYGL KSGLKKQELL EALTKHFQD

UniProtKB: X-ray repair cross-complementing protein 6

Macromolecule #2: X-ray repair cross-complementing protein 5

• Macromolecule: Name: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 82.812438 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS LGKEDGSGDR GDGPFRLGGH GPSFPLKGIT EQQKEGLEIV KMVMISLEGE DGLDEIYSFS ESLRKLCVFK KI ERHSIHW PCRLTIGSNL SIRIAAYKSI LQERVKKTWT VVDAKTLKKE DIQKETVYCL NDDDETEVLK EDIIQGFRYG SDI VPFSKV DEEQMKYKSE GKCFSVLGFC KSSQVQRRFF MGNQVLKVFA ARDDEAAAVA LSSLIHALDD LDMVAIVRYA YDKR ANPQV GVAFPHIKHN YECLVYVQLP FMEDLRQYMF SSLKNSKKYA PTEAQLNAVD ALIDSMSLAK KDEKTDTLED LFPTT KIPN PRFQRLFQCL LHRALHPREP LPPIQQHIWN MLNPPAEVTT KSQIPLSKIK TLFPLIEAKK KDQVTAQEIF QDNHED GPT AKKLKTEQGG AHFSVSSLAE GSVTSVGSVN PAENFRVLVK QKKASFEEAS NQLINHIEQF LDTNETPYFM KSIDCIR AF REEAIKFSEE QRFNNFLKAL QEKVEIKQLN HFWEIVVQDG ITLITKEEAS GSSVTAEEAK KFLAPKDKPS GDTAAVFE E GGDVDDLLDM I

UniProtKB: X-ray repair cross-complementing protein 5

Macromolecule #3: Non-homologous end-joining factor 1

• Macromolecule: Name: Non-homologous end-joining factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 33.625535 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKELNKRLTA PPAAFLCHLD NLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWNFHCMLA SPSLVSQHLI RPLMGMSLAL QCQVRELATL L HMKDLEIQ DYQESGATLI RDRLKTEPFE ENSFLEQFMI EKLPEACSIG DGKPFVMNLQ DLYMAVTTQE VQVGQKHQGA GD PHTSNSA SLQGIDSQCV NQPEQLVSSA PTLSAPEKES TGTSGPLQRP QLSKVKRKKP RGLFS

UniProtKB: Non-homologous end-joining factor 1

Macromolecule #4: DNA repair protein XRCC4

• Macromolecule: Name: DNA repair protein XRCC4 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 38.337703 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP AEVIRELICY CLDTIAENQA KNEHLQKENE RLLRDWNDVQ G RFEKCVSA KEALETDLYK RFILVLNEKK TKIRSLHNKL LNAAQEREKD IKQEGETAIC SEMTADRDPV YDESTDEESE NQ TDLSGLA SAAVSKDDSI ISSLDVTDIA PSRKRRQRMQ RNLGTEPKMA PQENQLQEKE NSRPDSSLPE TSKKEHISAE NMS LETLRN SSPEDLFDEI

UniProtKB: DNA repair protein XRCC4

Macromolecule #5: DNA ligase 4

• Macromolecule: Name: DNA ligase 4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 104.37825 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDVTDSFYPA MRLILPQLER ERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA S NNSAKRKD LIKKSLLQLI TQSSALEQKW LIRMIIKDLK LGVSQQTIFS VFHNDAAELH NVTTDLEKVC RQLHDPSVGL SD ISITLFS AFKPMLAAIA DIEHIEKDMK HQSFYIETKL DGERMQMHKD GDVYKYFSRN GYNYTDQFGA SPTEGSLTPF IHN AFKADI QICILDGEMM AYNPNTQTFM QKGTKFDIKR MVEDSDLQTC YCVFDVLMVN NKKLGHETLR KRYEILSSIF TPIP GRIEI VQKTQAHTKN EVIDALNEAI DKREEGIMVK QPLSIYKPDK RGEGWLKIKP EYVSGLMDEL DILIVGGYWG KGSRG GMMS HFLCAVAEKP PPGEKPSVFH TLSRVGSGCT MKELYDLGLK LAKYWKPFHR KAPPSSILCG TEKPEVYIEP CNSVIV QIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE QLRGKASGKL ASKHLYIGGD DEPQEKKRKA APKMKKV IG IIEHLKAPNL TNVNKISNIF EDVEFCVMSG TDSQPKPDLE NRIAEFGGYI VQNPGPDTYC VIAGSENIRV KNIILSNK H DVVKPAWLLE CFKTKSFVPW QPRFMIHMCP STKEHFAREY DCYGDSYFID TDLNQLKEVF SGIKNSNEQT PEEMASLIA DLEYRYSWDC SPLSMFRRHT VYLDSYAVIN DLSTKNEGTR LAIKALELRF HGAKVVSCLA EGVSHVIIGE DHSRVADFKA FRRTFKRKF KILKESWVTD SIDKCELQEE NQYLI

UniProtKB: DNA ligase 4

Macromolecule #6: Protein PAXX

• Macromolecule: Name: Protein PAXX / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 23.282197 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAALKARFGL SAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPRLRALT LGLAKRVWSL ERRLAAAEET A VSPRKSPR PAGPQLFLPD PDPQRGGPGP GVRRRCPGES LINPGFKSKK PAGGVDFDET

UniProtKB: Protein PAXX

Macromolecule #7: DNA (40-MER)

• Macromolecule: Name: DNA (40-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 20.722289 KDa

Sequence

String:

(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT)(DG)(DC) (DA) (DT)(DG)(DC)(DT)(DC)(DT)(DA)(DC) (DT)(DG)(DC)(DT)(DT)(DC)(DT)(DG)(DA)(DT) (DC)(DT) (DA)(DG)(DT)(DC)(DG)(DA)(DC) (DC)

Macromolecule #8: DNA (38-MER)

• Macromolecule: Name: DNA (38-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 20.811352 KDa

Sequence

String:

(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DA)(DT)(DT)(DC)(DG) (DT) (DT)(DC)(DA)(DC)(DG)(DT)(DG)(DA) (DG)(DT)(DT)(DC)(DC)(DA)(DG)(DT)(DA)(DC) (DA)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DT) (DC)

Macromolecule #9: DNA (36-MER)

• Macromolecule: Name: DNA (36-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.865188 KDa

Sequence

String:

(DG)(DA)(DC)(DT)(DA)(DG)(DA)(DT)(DC)(DA) (DG)(DA)(DA)(DG)(DC)(DA)(DG)(DT)(DA)(DG) (DA)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DA)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT) (DT) (DT)(DA)(DT)(DT)(DG)(DG)(DG)(DC) (DG)(DC)(DG)

Macromolecule #10: DNA (34-MER)

• Macromolecule: Name: DNA (34-MER) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.807135 KDa

Sequence

String:

(DA)(DG)(DA)(DC)(DT)(DT)(DG)(DT)(DA)(DC) (DT)(DG)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC) (DG)(DT)(DG)(DA)(DA)(DC)(DG)(DA)(DA) (DT)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT) (DT) (DT)(DA)(DT)(DT)(DG)(DG)(DG)(DC) (DG)(DC)(DG)

Macromolecule #11: ADENOSINE MONOPHOSPHATE

• Macromolecule: Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: AMP
• Molecular weight: Theoretical: 347.221 Da

Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.35 mg/mL
• Buffer: pH: 7.9
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.2 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Startup model

Type of model: EMDB MAP
EMDB ID:

23509

• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF; Details: The resolution is reported by the postprocess in RELION based on the composite half maps generated by phenix.combine_focused_maps.; Number images used: 500830
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD