- PDB-3rwr: Crystal structure of the human XRCC4-XLF complex -
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Basic information
Entry
Database: PDB / ID: 3rwr
Title
Crystal structure of the human XRCC4-XLF complex
Components
DNA repair protein XRCC4
Non-homologous end-joining factor 1
Keywords
DNA binding protein/protein binding / complex-filament / non-homologous end-joining / DNA and Protein Binding / DNA binding protein-protein binding complex
Function / homology
Function and homology information
FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / response to ionizing radiation ...FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / response to ionizing radiation / cellular response to lithium ion / 2-LTR circle formation / T cell differentiation / response to X-ray / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / B cell differentiation / central nervous system development / Nonhomologous End-Joining (NHEJ) / fibrillar center / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function
Helix hairpin bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / : / XLF, N-terminal / XLF N-terminal domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain ...Helix hairpin bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / : / XLF, N-terminal / XLF N-terminal domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / DNA repair protein XRCC4 / Non-homologous end-joining factor 1 Similarity search - Component
The biological assembly is a filament of alternating homodimers of XRCC4 and XLF. The unit is assembled by the following chains: GF, IH, BA, ED. This has been confirmed by SAXS (Hammel, M., Yu, Y., Fang, S., Lees-Miller, S.P., and Tainer, J.A. (2010). XLF regulates filament architecture of the XRCC4-ligaseIV complex. Structure. 11, 1431-1442.).
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Components
#1: Protein
DNArepairproteinXRCC4 / X-ray repair cross-complementing protein 4
Mass: 18869.123 Da / Num. of mol.: 12 / Fragment: unp residues 1-157 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q13426
#2: Protein
Non-homologousend-joiningfactor1 / Protein cernunnos / XRCC4-like factor
Mass: 26286.348 Da / Num. of mol.: 12 / Fragment: unp residues 1-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9H9Q4
Method to determine structure: molecular replacement-SAD / Resolution: 3.943→49.027 Å / SU ML: 1.55 / σ(F): 0 / Phase error: 36.08 / Stereochemistry target values: MLHL Details: THE TA ATOM FOR CHAINS P AND V HAS BEEN REFINED WITH OCCUPANCY HIGHER THAN 1.0.
Rfactor
Num. reflection
% reflection
Rfree
0.3256
3879
5.03 %
Rwork
0.2707
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obs
0.2735
77191
99.14 %
all
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77252
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Solvent computation
Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 157.435 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-58.2565 Å2
0 Å2
-37.7716 Å2
2-
-
44.8642 Å2
-0 Å2
3-
-
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13.3923 Å2
Refinement step
Cycle: LAST / Resolution: 3.943→49.027 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
36689
0
144
0
36833
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
37747
X-RAY DIFFRACTION
f_angle_d
0.788
50670
X-RAY DIFFRACTION
f_dihedral_angle_d
19.53
13882
X-RAY DIFFRACTION
f_chiral_restr
0.065
5660
X-RAY DIFFRACTION
f_plane_restr
0.003
6519
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.9427-3.9907
0.4165
95
0.3931
2157
X-RAY DIFFRACTION
81
3.9907-4.0412
0.4149
151
0.3809
2644
X-RAY DIFFRACTION
100
4.0412-4.0944
0.4066
139
0.3621
2532
X-RAY DIFFRACTION
100
4.0944-4.1504
0.4285
137
0.3556
2683
X-RAY DIFFRACTION
100
4.1504-4.2097
0.3781
123
0.3287
2624
X-RAY DIFFRACTION
100
4.2097-4.2725
0.3545
152
0.3223
2631
X-RAY DIFFRACTION
100
4.2725-4.3392
0.3555
134
0.2915
2557
X-RAY DIFFRACTION
100
4.3392-4.4103
0.3134
128
0.2671
2660
X-RAY DIFFRACTION
100
4.4103-4.4863
0.3318
136
0.2591
2696
X-RAY DIFFRACTION
100
4.4863-4.5678
0.3209
120
0.2602
2602
X-RAY DIFFRACTION
100
4.5678-4.6556
0.2949
126
0.2376
2615
X-RAY DIFFRACTION
100
4.6556-4.7506
0.3181
149
0.2449
2665
X-RAY DIFFRACTION
100
4.7506-4.8538
0.3134
128
0.2379
2590
X-RAY DIFFRACTION
100
4.8538-4.9666
0.2896
134
0.2442
2647
X-RAY DIFFRACTION
100
4.9666-5.0907
0.3269
144
0.2498
2613
X-RAY DIFFRACTION
100
5.0907-5.2281
0.3129
123
0.252
2642
X-RAY DIFFRACTION
100
5.2281-5.3818
0.3989
150
0.2787
2681
X-RAY DIFFRACTION
100
5.3818-5.5553
0.3948
144
0.3402
2573
X-RAY DIFFRACTION
100
5.5553-5.7535
0.4465
164
0.367
2665
X-RAY DIFFRACTION
100
5.7535-5.9835
0.3853
140
0.3558
2584
X-RAY DIFFRACTION
100
5.9835-6.2553
0.4025
148
0.3676
2677
X-RAY DIFFRACTION
100
6.2553-6.5844
0.4378
146
0.3594
2611
X-RAY DIFFRACTION
100
6.5844-6.9958
0.3842
126
0.3276
2640
X-RAY DIFFRACTION
100
6.9958-7.5342
0.4006
142
0.2813
2667
X-RAY DIFFRACTION
100
7.5342-8.2891
0.2735
170
0.2102
2630
X-RAY DIFFRACTION
100
8.2891-9.4811
0.2229
145
0.1666
2665
X-RAY DIFFRACTION
100
9.4811-11.9167
0.2029
150
0.1714
2637
X-RAY DIFFRACTION
99
11.9167-49.0304
0.337
135
0.3011
2724
X-RAY DIFFRACTION
99
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