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- PDB-9pd4: NER dual incision complex - DuIM -

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Basic information

Entry
Database: PDB / ID: 9pd4
TitleNER dual incision complex - DuIM
Components
  • (DNA excision repair protein ERCC- ...) x 2
  • (General transcription factor IIH subunit ...) x 5
  • (Replication protein A ...) x 3
  • DNA
  • DNA (Cy5)
  • DNA repair endonuclease XPF
  • DNA repair protein complementing XP-A cells
  • General transcription and DNA repair factor IIH helicase subunit XPD
  • TFIIH basal transcription factor complex helicase XPB subunit
KeywordsDNA BINDING PROTEIN/DNA / NER / XPA / XPG / XPF / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of t-circle formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / protein localization to chromosome / nucleotide-excision repair, DNA damage recognition / DNA replication factor A complex / nucleotide-excision repair complex ...positive regulation of t-circle formation / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / protein localization to chromosome / nucleotide-excision repair, DNA damage recognition / DNA replication factor A complex / nucleotide-excision repair complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / negative regulation of telomere maintenance / Cytosolic iron-sulfur cluster assembly / single-stranded DNA endonuclease activity / base-excision repair, AP site formation / resolution of meiotic recombination intermediates / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / t-circle formation / CAK-ERCC2 complex / bubble DNA binding / mitotic recombination / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / lateral element / G-rich strand telomeric DNA binding / regulation of cyclin-dependent protein serine/threonine kinase activity / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / G protein-coupled receptor internalization / response to UV-C / hydrolase activity, acting on ester bonds / DNA 5'-3' helicase / nuclear thyroid hormone receptor binding / Removal of the Flap Intermediate from the C-strand / chromatin-protein adaptor activity / transcription preinitiation complex / RNA Polymerase I Transcription Termination / embryonic organ development / negative regulation of telomere maintenance via telomere lengthening / UV-damage excision repair / transcription factor TFIID complex / regulation of double-strand break repair via homologous recombination / RNA polymerase II general transcription initiation factor activity / male germ cell nucleus / regulation of DNA damage checkpoint / telomeric repeat DNA binding / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HDR through Single Strand Annealing (SSA) / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / ATPase activator activity / DNA topological change / RNA polymerase II complex binding / RNA Polymerase I Transcription Initiation / response to UV / Impaired BRCA2 binding to RAD51 / TFIID-class transcription factor complex binding / DNA 3'-5' helicase / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / 3'-5' DNA helicase activity / HSF1 activation / Presynaptic phase of homologous DNA pairing and strand exchange / Tat-mediated elongation of the HIV-1 transcript / telomere maintenance via telomerase / Formation of HIV-1 elongation complex containing HIV-1 Tat / Activation of ATR in response to replication stress / mismatch repair / SUMOylation of DNA damage response and repair proteins / Formation of HIV elongation complex in the absence of HIV Tat / hormone-mediated signaling pathway / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / mitotic G1 DNA damage checkpoint signaling / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / transcription-coupled nucleotide-excision repair / telomere maintenance / DNA helicase activity / Translesion synthesis by REV1
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / DNA repair protein XPF / Replication factor A protein 2 / Replication protein A, C-terminal / : / Replication protein A C terminal / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal ...XPG/Rad2 endonuclease, eukaryotes / DNA repair protein XPF / Replication factor A protein 2 / Replication protein A, C-terminal / : / Replication protein A C terminal / ERCC1/RAD10/SWI10 family / : / Binding domain of DNA repair protein Ercc1 (rad10/Swi10) / XPA protein N-terminal / Replication factor A protein 3 / Replication factor A protein 3 / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / Replication factor-A protein 1, N-terminal domain / Replication factor A protein-like / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / ERCC4 domain / ERCC4 domain / ERCC4 domain / : / XPG protein signature 2. / Replication factor A, C-terminal / Replication factor-A C terminal domain / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ERCC3/RAD25/XPB helicase, C-terminal domain / : / Ubiquitin-binding motif (UBM) domain profile. / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Putative DNA-binding domain superfamily / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / RuvA domain 2-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Restriction endonuclease type II-like / OB-fold nucleic acid binding domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / PIN-like domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / :
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA excision repair protein ERCC-1 / Replication protein A 32 kDa subunit / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / Replication protein A 70 kDa DNA-binding subunit / DNA excision repair protein ERCC-5 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA excision repair protein ERCC-1 / Replication protein A 32 kDa subunit / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / Replication protein A 70 kDa DNA-binding subunit / DNA excision repair protein ERCC-5 / General transcription factor IIH subunit 1 / Replication protein A 14 kDa subunit / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4 / DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, C.L. / Kim, J. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK075037 United States
CitationJournal: Nature / Year: 2026
Title: Pre-incision structures reveal principles of DNA nucleotide excision repair.
Authors: Eric C L Li / Jinseok Kim / Sem J Brussee / Kaoru Sugasawa / Martijn S Luijsterburg / Wei Yang /
Abstract: Nucleotide excision repair (NER) removes bulky adducts from genomic DNA and prevents the ultraviolet light-sensitivity disease xeroderma pigmentosum, cancer and premature ageing. After initial lesion ...Nucleotide excision repair (NER) removes bulky adducts from genomic DNA and prevents the ultraviolet light-sensitivity disease xeroderma pigmentosum, cancer and premature ageing. After initial lesion recognition by XPC in global genome repair or by stalled RNA polymerases in transcription-coupled repair, a lesion and surrounding DNA duplex are unwound by TFIIH, which includes the ATPases XPB and XPD, and additional NER factors XPA, XPF, XPG and RPA, to form a DNA bubble comprising around 27 nucleotides. The double strand-single strand (ds-ss) junction-specific endonucleases XPF and XPG cleave DNA on the 5' and 3' sides of the lesion, respectively. Here we report the functional steps and atomic structures of the ATPase-driven and lesion-dependent DNA bubble formation and arrangement of the complete NER factors for dual incision. The unwinding of nearly 30 base pairs of DNA depends mainly on the double strand DNA translocase XPB and the duplex dividers XPA and XPF. XPD binds the lesion strand with XPF at the 5' ds-ss junction. XPF cuts the lesion strand only after XPG binds the 3' ds-ss junction. The ERCC1 subunit of XPF facilitates DNA strand separation and recruitment of RPA to the non-lesion strand. These findings provide insights on the causes of human diseases and potential targets for enhancing chemotherapeutic efficacy.
History
DepositionJun 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
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Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 2.0May 27, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_src_syn / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine_ls_restr / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.entity_id / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly.type / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.entity_id / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.i_label_asym_id / _ndb_struct_na_base_pair.j_label_asym_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_label_asym_id_1 / _ndb_struct_na_base_pair_step.i_label_asym_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_label_asym_id_1 / _ndb_struct_na_base_pair_step.j_label_asym_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entity_src_syn.entity_id / _pdbx_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet.id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id
Description: Model orientation/position
Details: We discovered that the assignment of p62 chain C:397-436 was incorrect and exhibited a helical shift. We have corrected the model based on the 8EBS structure.
Provider: author / Type: Coordinate replacement
Revision 1.3May 27, 2026Data content type: EM metadata
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Item: _em_admin.last_update / _em_entity_assembly.entity_id_list ..._em_admin.last_update / _em_entity_assembly.entity_id_list / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly.type / _entity_src_gen.entity_id / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_entity_src_syn.entity_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Revision 2.1Aug 12, 2026Group: Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_entry_details ...em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Description: Metalloprotein remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TFIIH basal transcription factor complex helicase XPB subunit
B: General transcription and DNA repair factor IIH helicase subunit XPD
C: General transcription factor IIH subunit 1
D: General transcription factor IIH subunit 4, p52
E: General transcription factor IIH subunit 2
F: General transcription factor IIH subunit 3
G: General transcription factor IIH subunit 5
K: DNA repair protein complementing XP-A cells
L: DNA (Cy5)
M: DNA
N: Replication protein A 70 kDa DNA-binding subunit
O: Replication protein A 32 kDa subunit
P: Replication protein A 14 kDa subunit
Q: DNA repair endonuclease XPF
R: DNA excision repair protein ERCC-1
S: DNA excision repair protein ERCC-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)850,52024
Polymers849,71016
Non-polymers8108
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules ABKQ

#1: Protein TFIIH basal transcription factor complex helicase XPB subunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA ...Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 89404.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19447, DNA helicase
#2: Protein General transcription and DNA repair factor IIH helicase subunit XPD / TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision ...TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 88018.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18074, DNA helicase
#8: Protein DNA repair protein complementing XP-A cells / Xeroderma pigmentosum group A-complementing protein


Mass: 31422.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P23025
#14: Protein DNA repair endonuclease XPF / DNA excision repair protein ERCC-4 / DNA repair protein complementing XP-F cells / Xeroderma ...DNA excision repair protein ERCC-4 / DNA repair protein complementing XP-F cells / Xeroderma pigmentosum group F-complementing protein


Mass: 104694.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC4, ERCC11, XPF / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q92889, Hydrolases; Acting on ester bonds

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General transcription factor IIH subunit ... , 5 types, 5 molecules CDEFG

#3: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 62116.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32780
#4: Protein General transcription factor IIH subunit 4, p52 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92759
#5: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44481.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13888
#6: Protein General transcription factor IIH subunit 3 / p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 34416.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13889
#7: Protein General transcription factor IIH subunit 5 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6ZYL4

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DNA chain , 2 types, 2 molecules LM

#9: DNA chain DNA (Cy5)


Mass: 28705.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain DNA


Mass: 29180.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Replication protein A ... , 3 types, 3 molecules NOP

#11: Protein Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 68212.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P27694
#12: Protein Replication protein A 32 kDa subunit / RP-A p32 / Replication factor A protein 2 / RF-A protein 2 / Replication protein A 34 kDa subunit / RP-A p34


Mass: 29276.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA2, REPA2, RPA32, RPA34 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P15927
#13: Protein Replication protein A 14 kDa subunit / RP-A p14 / Replication factor A protein 3 / RF-A protein 3


Mass: 13583.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA3, REPA3, RPA14 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P35244

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DNA excision repair protein ERCC- ... , 2 types, 2 molecules RS

#15: Protein DNA excision repair protein ERCC-1


Mass: 32402.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P07992
#16: Protein DNA excision repair protein ERCC-5 / DNA repair protein complementing XP-G cells / XPG / Xeroderma pigmentosum group G-complementing protein


Mass: 133489.562 Da / Num. of mol.: 1 / Mutation: D812N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC5, ERCM2, XPG, XPGC / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P28715, Hydrolases; Acting on ester bonds

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Non-polymers , 2 types, 8 molecules

#17: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NER dual incision complex / Type: COMPLEX / Entity ID: #1-#7, #16, #14-#15, #8-#13 / Source: RECOMBINANT
Molecular weightValue: 0.8 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMpotassium acetateKOAc1
225 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris1
32 mMcalcium chlorideCaCl21
42 mM(Tris(2-carboxyethyl)phospine)TCEP1
51 %glycerolGlycerol1
60.05 %Octyl glucosideC14H28O61
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 52.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 6 / Num. of real images: 52926

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9PHENIX1.21rc1_5127model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140332 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetails (eV)Initial refinement model-ID
18ebt

8ebt

8ebtC7CAD1
26sxa

6sxa

6sxaXPF/ERCC1
31l1o

1l1o

1l1oRPA trimerization core
41jmc

1jmc

1jmcRPA70
56tus

6tus

6tusXPG catalytic domain
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00241105
ELECTRON MICROSCOPYf_angle_d0.4456035
ELECTRON MICROSCOPYf_dihedral_angle_d14.38515633
ELECTRON MICROSCOPYf_chiral_restr0.0386286
ELECTRON MICROSCOPYf_plane_restr0.0036824

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