PDBIHM.org

PDB-IHM

System for Archiving Integrative Structures

2.1. Ensemble information?

This entry consists of 0 distinct ensemble.

2.2. Representation ?

This entry has 1 representation(s).

ID Model(s) Entity ID Molecule name Chain(s) [auth] Total residues Rigid segments Flexible segments Model coverage/
Starting model coverage
(%)		 Scale
1 1 1 General transcription and DNA repair factor IIH helicase subunit XPB A 720 - 34-203, 248-720 89.31 /
100.00 		Atomic
2 General transcription and DNA repair factor IIH helicase subunit XPD B 760 - 1-760 100.00 /
0.00 		Atomic
3 General transcription factor IIH subunit 4 C 441 - 1-441 100.00 /
100.00 		Atomic
4 General transcription factor IIH subunit 2 D 377 - 1-377 100.00 /
100.00 		Atomic
5 General transcription factor IIH subunit 3 E 292 - 1-292 100.00 /
0.00 		Atomic
6 General transcription factor IIH subunit 5 F 66 - 1-66 100.00 /
100.00 		Atomic
7 DNA repair protein complementing XP-A cells G 273 - 1-273 100.00 /
0.00 		Atomic
8 General transcription factor IIH subunit 1 H 154 - 1-154 100.00 /
100.00 		Atomic
9 DNA excision repair protein ERCC-5 I 985 - 1-296, 733-985 55.74 /
100.00 		Atomic
10 DNA repair endonuclease XPF Gene: ERCC4, ERCC11, XPF J 227 - 1-227 100.00 /
100.00 		Atomic
11 DNA excision repair K 198 - 1-198 100.00 /
100.00 		Atomic
12 Replication protein A 70 kDa DNA-binding subunit, N-terminally processed L 434 - 1-434 100.00 /
100.00 		Atomic
13 Replication protein A 14 kDa subunit M 115 - 1-115 100.00 /
100.00 		Atomic
14 Replication protein A 32 kDa subunit N 225 - 1-225 100.00 /
100.00 		Atomic
15 DNA (66-MER) O [X] 66 - 1-66 100.00 /
100.00 		Atomic
16 DNA (66-MER) P [Y] 66 - 1-66 100.00 /
100.00 		Atomic
17 IRON/SULFUR CLUSTER Q [B] Non-polymeric - - Not available /
Not available 		Atomic
18 ZINC ION R [D] Non-polymeric - - Not available /
Not available 		Atomic
S [D]
T [D]
U [E]
V [E]
W [G]
Z [L]
19 MAGNESIUM ION X [I] Non-polymeric - - Not available /
Not available 		Atomic
Y [J]
20 water AA [Y] Non-polymeric - - Not available /
Not available 		Atomic

2.3. Datasets used for modeling ?

There are 25 unique datasets used to build the models in this entry.
ID Dataset type Database name Data access code
1
Experimental model
PDB
2
3DEM volume
EMDB
3
Experimental model
PDB
4
Crosslinking-MS data
Not available
5
De Novo model
Not available
Not available
6
De Novo model
Not available
Not available
7
De Novo model
Not available
Not available
8
Experimental model
PDB
9
Experimental model
PDB
10
Experimental model
PDB
11
De Novo model
Not available
Not available
12
Experimental model
PDB
13
Experimental model
PDB
14
Experimental model
PDB
15
Experimental model
PDB
16
Experimental model
PDB
17
Experimental model
PDB
18
De Novo model
Not available
Not available
19
De Novo model
Not available
Not available
20
De Novo model
Not available
Not available
21
De Novo model
Not available
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22
De Novo model
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23
De Novo model
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24
De Novo model
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25
De Novo model
MODEL ARCHIVE

2.4. Methodology and software?

This entry is a result of 1 distinct protocol.
Step number Protocol ID Method name Method type Method description Number of computed models Multi state modeling Multi scale modeling
1
1
Not available
Not available
To construct a model of the pre-incision complex (PlnC), we systematically examined the cryo-EM structures and densities of human apo-TFIIH, TFIIH/XPA/DNA, and XPF/ERCC1, the NMR structure of XPA-ERCC1, and the X-ray structures of the XPG catalytic core and RPA-ssDNA (RPA70, RPA32, and RPA14). The TFIIH/XPA/DNA structure (PDB ID: 6RO4 and EMDB accession code: EMD-4970) was the starting point for model building. The PInC hybrid model has an NER bubble size of 23 nucleotides, matching the 27-nucleotide optimal length of the excision products and the XPF and XPG incision patterns. FEN1 shares 30% sequence identity with the XPG catalytic core (PDB ID: 6TUR, 6TUW, and 6VBH). Thus, we modeled DNA-bound XPG based on the human FEN1/DNA X-ray structure (PDB ID: 5UM9). XPG positioning into the hybrid model was based on existing XL-MS data. In addition, positioning of the XPG core required placement of the 3' DNA junction 8 nucleotides away from the expected position of the DNA lesion near XPD's His135 residue. The two XPG gateway helices (GH1, residues 82-126) and (GH2, residues 734-761) were predicted with AlphaFold2 and positioned in the gap between XPD's Arch and Fe-S domains in accordance with the crosslink data. The XPD-anchor domain (residues 157-296) was predicted by AlphaFold2 and fitted into the TFIIH/XPA/DNA cryo-EM density. The loop connecting GH1 and the XPD-anchor was built with Modeller. To model XPF/ERCC1, we used the cryo-EM structures of XPF/ERCC1 (PDB ID: 6SXA and 6SXB). We first docked the XPF nuclease domain to the 5' junction. The catalytic metal was oriented 3A away from the scissile phosphodiester bond. Mg2+ ion coordination was based on the Aeropyrum pernix SNF2 structure (PDB ID: 2BGW). A water molecule was placed between Mg2+ ion and the DNA backbone phosphate group. The ERCC1 (HhH)2 domain was oriented to interact with the ssDNA through two DNA hairpins based on the 6SXB structure. The long linkers from the ERCC1 central domain to the ERCC1 (HhH)2 (residues 214-230) and from the XPF nuclease domain to the XPF (HhH)2 (residues 817-847) were built with Modeller. The SF2 helicase-like N-terminal domain of XPF was omitted from the hybrid PInC model due to lack of sufficient structural or biochemical restraints. To model RPA, we used following X-ray structures: Ustilago maydis RPA/ssDNA (PDB ID: 4GOP), yeast RPA/ssDNA (PDB ID: 6I52) and human RPA (PDB ID: 1JMC and 1L1O). The RPA70AB/ssDNA complex was modeled by superimposing the yeast RPA/ssDNA structure (PDB ID: 1JMC) onto the human apo-RPA 70AB (PDB ID: 6I52). Within PInC, only RPA70A, 70B, and 70C can engage DNA due to the size of the NER bubble. RPA70AB was placed close to the 3' junction where it interacts with XPG. We reoriented RPA70C to bind ssDNA near the 5' junction. The RPA70C/ssDNA was modeled by aligning the Ustilago maydis RPA/ssDNA structure (PDB ID: 4GOP) with the human trimer core structure (PDB ID: 1L1O). The orientation of RPA32D and RPA14 follows from the placement of the RPA70C module as they are all connected, forming the trimer core (70C/32D/14). To model XPA, we used the following structures: the cryo-EM TFIIH/XPA/DNA structure (PDB ID: 6RO4), the NMR structure of XPA/ERCC1 (PDB ID: 2JNW), and the human X-ray structure of RPA32C/Smarcal1 N-terminus (PDB ID: 4MQV). The XPA N-terminal extension (residues 1-103), which includes the RPA32C binding helix (residues 22-40), and the C-terminal extension (beta-domain) (residues 235-273) lacked known structural homologues and were modeled using AlphaFold2. The beta-domain was fitted into the TFIIH/XPA/DNA density. To position XPA's N-terminal helix (residues 22-40) we used the X-ray structure of RPA32C/Smarcal1 N-terminus. To assemble the complete PInC model, we also modelled loop regions of TFIIH's core subunits (XPB, XPD, p44, p34, and p52) into the TFIIH/XPA/DNA density.
Not available
False
False
There are 6 software packages reported in this entry.
ID Software name Software version Software classification Software location
1
Not available
model building
2
10.40
model building
3
Not available
sequence alignments
4
0.9.8.92
real-space refinement
5
1.20.1
real-space refinement
6
1.18
model visualization