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6t4b

CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 96.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TAR DNA-binding protein 43

Homo sapiens

UniProt Q13148

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–80 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Sodium bromide, 0.1M Bis-Tris propane 6.5, 20% PEG 3350 Resolution 2.55 Å R-free 0.263
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–80 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Sodium bromide, 0.1M Bis-Tris propane 6.5, 20% PEG 3350 Resolution 2.55 Å R-free 0.263
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 1–80 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Sodium bromide, 0.1M Bis-Tris propane 6.5, 20% PEG 3350 Resolution 2.55 Å R-free 0.263
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain G； UniProt 1–80 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Sodium bromide, 0.1M Bis-Tris propane 6.5, 20% PEG 3350 Resolution 2.55 Å R-free 0.263
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain I； UniProt 1–80 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M Sodium bromide, 0.1M Bis-Tris propane 6.5, 20% PEG 3350 Resolution 2.55 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6T4B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WF0 Solution structure of RRM domain in TAR DNA-binding protein-43 Deposited 2004-05-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 193–267（75 aa） Fragment：RRM domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 0.8mM U-15, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2CQG Solution structure of the RNA binding domain of TAR DNA-binding protein-43 Deposited 2005-05-20 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 96–185（90 aa） Fragment：RNA recognition motif
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 0.86mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 | 90% H2O/10% D2O
Resolution not provided
2N2C NMR Structure of TDP-43 prion-like hydrophobic helix in DPC Deposited 2015-05-06 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 307–349（43 aa） Fragment：UNP residues 307-349
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；313 K；Ionic strength (raw mmCIF value) 1；Pressure ambient
NMR sample composition 300 uM [U-100% 15N] entity-1, 60 mM DPC-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N3X Solution Structure of TDP-43 Amyloidogenic Core Region Deposited 2015-06-11 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 311–360（50 aa） Fragment：UNP residues 311-360
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 80；Pressure ambient
NMR sample composition 600 uM [U-99% 13C; U-99% 15N] GB1-TDP(311 - 360)-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 8 v/v [U-99% 2H] D2O-4, 0.02 v/v sodium azide-5, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2N4G Solution Structure of the G335D Mutant of TDP-43 Amyloidogenic Core Region Deposited 2015-06-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 311–360（50 aa） Fragment：UNP residues 311-360
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 80；Pressure ambient
NMR sample composition 600 uM [U-99% 13C; U-99% 15N] GB1-TDP(311-360)-G335D-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 8 % [U-99% 2H] D2O-4, 0.02 w/v sodium azide-5, 92 % H2O-6, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2N4H Solution Structure of the Q343R Mutant of TDP-43 Amyloidogenic Core Region Deposited 2015-06-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 311–360（50 aa） Fragment：UNP residues 311-360
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 80；Pressure ambient
NMR sample composition 600 uM [U-99% 13C; U-99% 15N] GB1-TDP(311-360)-Q343R-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 0.02 w/v sodium azide-4, 8 % [U-99% 2H] D2O-5, 92 % H2O-6, 92% H2O/8% D2O | 92% H2O/8% D2O
Resolution not provided
2N4P Solution structure of the n-terminal domain of tdp-43 Deposited 2015-06-26 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–77（77 aa） Fragment：N-terminal residues 1-77
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.8；298 K；Pressure ambient
NMR sample composition 0.5-0.7 mM [U-13C; U-15N] NTD, TCEP, CD3COOD/ CD3COO-Na+, NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4BS2 NMR structure of human TDP-43 tandem RRMs in complex with UG-rich RNA Deposited 2013-06-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 102–269（168 aa） Fragment：RNA BINDING DOMAIN, RESIDUES 102-269
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50
NMR sample composition 94%WATER/6%D2O
Resolution not provided
4IUF Crystal Structure of Human TDP-43 RRM1 Domain in Complex with a Single-stranded DNA Deposited 2013-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 103–179（77 aa） Fragment：RRM1 Domain (UNP residues 103-179)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.12M CH3COONH4, 0.05M Bis-Tris, 16% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.75 Å R-free 0.259
4Y00 Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA Deposited 2015-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 101–191（91 aa） Fragment：UNP residues 101-191
Mutation：D169G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.05 M CH3COONH4, pH 5.0, 15% v/v Jeffamine ED-2001, pH 7.0
Resolution 3.00 Å R-free 0.295
4Y00 Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA Deposited 2015-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 101–191（91 aa） Fragment：UNP residues 101-191
Mutation：D169G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.05 M CH3COONH4, pH 5.0, 15% v/v Jeffamine ED-2001, pH 7.0
Resolution 3.00 Å R-free 0.295
4Y00 Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA Deposited 2015-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 101–191（91 aa） Fragment：UNP residues 101-191
Mutation：D169G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.05 M CH3COONH4, pH 5.0, 15% v/v Jeffamine ED-2001, pH 7.0
Resolution 3.00 Å R-free 0.295
4Y00 Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA Deposited 2015-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain D 101–191（91 aa） Fragment：UNP residues 101-191
Mutation：D169G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.05 M CH3COONH4, pH 5.0, 15% v/v Jeffamine ED-2001, pH 7.0
Resolution 3.00 Å R-free 0.295
4Y0F Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified Single-stranded DNA Deposited 2015-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 101–191（91 aa） Fragment：UNP residues 101-191
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.12M ammonium acetate, 0.08M BIS-TRIS, pH 5.5, 20% PEG 3350
Resolution 2.65 Å R-free 0.288
4Y0F Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified Single-stranded DNA Deposited 2015-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 101–191（91 aa） Fragment：UNP residues 101-191
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.12M ammonium acetate, 0.08M BIS-TRIS, pH 5.5, 20% PEG 3350
Resolution 2.65 Å R-free 0.288
5MRG Solution structure of TDP-43 (residues 1-102) Deposited 2016-12-22 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–102（102 aa） Fragment：N-terminal domain, UNP residues 1-102
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.9；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.35 mM 13C15N TDP-43(1-102), 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5W50 Crystal structure of the segment, LIIKGI, from the RRM2 of TDP-43, residues 248-253 Deposited 2017-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 248–253（6 aa） Fragment：RRM2 peptide (UNP residues 248-253)
Chain B 248–253（6 aa） Fragment：RRM2 peptide (UNP residues 248-253)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；100 mM CHES, pH 9.5, 20% PEG8000, 10 mM lithium hydroxide
Resolution 1.40 Å R-free 0.207
5W52 MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257 Deposited 2017-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
X-ray crystallization conditions BATCH；pH 8.5；310 K；50 mM CHES, pH 8.5
Resolution 1.40 Å R-free 0.306
5W7V CryoEM structure of the segment, DLIIKGISVHI, assembled into a triple-helical fibril Deposited 2017-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 270 PDB declaration: 270-meric
Chain 0 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 1 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 2 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 3 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 4 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 5 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 6 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 7 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 8 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5W7V CryoEM structure of the segment, DLIIKGISVHI, assembled into a triple-helical fibril Deposited 2017-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric
Chain 0 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 1 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 2 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 3 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 4 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 5 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 6 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 7 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 8 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5W7V CryoEM structure of the segment, DLIIKGISVHI, assembled into a triple-helical fibril Deposited 2017-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric
Chain 0 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 1 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 2 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 3 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 4 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 5 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 6 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 7 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Chain 8 247–257（11 aa） Fragment：RRM2 peptide (UNP residues 247-257)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5WHN Crystal structure of the segment, NFGAFS, from the low complexity domain of TDP-43, residues 312-317 Deposited 2017-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 312–317（6 aa） Fragment：UNP residues 312-317
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；100mM phosphate/citrate 4.2, 40% ethanol, 5% PEG 1000
Resolution 1.10 Å R-free 0.160
5WHP Crystal structure of the segment, NFGTFS, from the A315T familial variant of the low complexity domain of TDP-43, residues 312-317 Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 312–317（6 aa） Fragment：UNP residues 312-317
Mutation：A315T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；100mM sodium acetate 4.6, 200mM ammonium acetate, 30% PEG 4000
Resolution 1.00 Å R-free 0.093
5WIA Crystal structure of the segment, GNNSYS, from the low complexity domain of TDP-43, residues 370-375 Deposited 2017-07-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 370–375（6 aa） Fragment：UNP residues 370-375
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100mM bis tris propane 8.5, 200mM sodium nitrate, 20% PEG 3350
Resolution 1.00 Å R-free 0.181
5WIQ Crystal structure of the segment, GFNGGFG, from the low complexity domain of TDP-43, residues 396-402 Deposited 2017-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 396–402（7 aa） Fragment：UNP residues 396-402
Chain B 396–402（7 aa） Fragment：UNP residues 396-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；100mM sodium acetate pH 4.5, 800mM sodium phosphate monobasic, 1200mM potassium phosphate dibasic
Resolution 1.25 Å R-free 0.168
5WKB MicroED structure of the segment, NFGEFS, from the A315E familial variant of the low complexity domain of TDP-43, residues 312-317 Deposited 2017-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 312–317（6 aa） Fragment：UNP residues 312-317
Mutation：A315E No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer pH 7.5；1x PBS, pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
X-ray crystallization conditions Batch；pH 7.5；298 K；1x PBS, pH 7.5
Resolution 1.00 Å R-free 0.270
5WKD Crystal structure of the segment, GNNQGSN, from the low complexity domain of TDP-43, residues 300-306 Deposited 2017-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 300–306（7 aa） Fragment：UNP residues 300-306
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM Bis-Tris propane, pH 7.5, 200 mM sodium sulfate, 20% PEG3350
Resolution 1.80 Å R-free 0.195
5X4F Solution Structure of the N-terminal Domain of TDP-43 Deposited 2017-02-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：C39S/C50S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure 1
NMR sample composition 1 mM U-99% 13C; U-99% 15N TDP(1-77)-GB1-C39/C50S, 20 mM sodium phosphate, 50 mM sodium chloride, 0.05 v/v sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6B1G Solution structure of TDP-43 N-terminal domain dimer. Deposited 2017-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–80（80 aa） Fragment：NTD domain
Chain B 1–80（80 aa） Fragment：NTD domain
Mutation：S48E Mutation：Y4R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.7 mM [U-99% 13C; U-99% 15N] TDP-43 NTD S48E, 2.0 mM TDP-43 NTD Y4R, 20 mM HEPES, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-99% 13C; U-99% 15N] TDP-43 NTD Y4R, 2 mM TDP-43 NTD S48E, 20 mM HEPES, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6CFH SWGMMGMLASQ segment from the low complexity domain of TDP-43 Deposited 2018-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric
Chain A 333–343（11 aa） Fragment：SWGMMGMLASQ segment
Chain B 333–343（11 aa） Fragment：SWGMMGMLASQ segment
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
X-ray crystallization conditions Batch；pH 7.5；303 K；phosphate buffered saline, shaken for 80 hours
Resolution 1.50 Å R-free 0.313
6N37 SegA-sym, conformation of TDP-43 low complexity domain segment A sym Deposited 2018-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 195–244（50 aa）
Chain B 195–244（50 aa）
Chain C 195–244（50 aa）
Chain D 195–244（50 aa）
Chain E 195–244（50 aa）
Chain F 195–244（50 aa）
Chain G 195–244（50 aa）
Chain H 195–244（50 aa）
Chain I 195–244（50 aa）
Chain J 195–244（50 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N3A SegA-long, conformation of TDP-43 low complexity domain segment A long Deposited 2018-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain A 195–244（50 aa）
Chain B 195–244（50 aa）
Chain C 195–244（50 aa）
Chain D 195–244（50 aa）
Chain E 195–244（50 aa）
Chain F 195–244（50 aa）
Chain G 195–244（50 aa）
Chain H 195–244（50 aa）
Chain I 195–244（50 aa）
Chain J 195–244（50 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6N3B SegA-asym, conformation of TDP-43 low complexity domain segment A asym Deposited 2018-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 195–244（50 aa）
Chain B 195–244（50 aa）
Chain C 195–244（50 aa）
Chain D 195–244（50 aa）
Chain E 195–244（50 aa）
Chain F 195–244（50 aa）
Chain G 195–244（50 aa）
Chain H 195–244（50 aa）
Chain I 195–244（50 aa）
Chain J 195–244（50 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N3C SegB, conformation of TDP-43 low complexity domain segment A Deposited 2018-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric
Chain A 170–215（46 aa）
Chain B 170–215（46 aa）
Chain C 170–215（46 aa）
Chain D 170–215（46 aa）
Chain E 170–215（46 aa）
Chain F 170–215（46 aa）
Chain G 170–215（46 aa）
Chain H 170–215（46 aa）
Chain I 170–215（46 aa）
Chain J 170–215（46 aa）
Chain K 170–215（46 aa）
Chain L 170–215（46 aa）
Chain M 170–215（46 aa）
Chain N 170–215（46 aa）
Chain O 170–215（46 aa）
Chain P 170–215（46 aa）
Chain Q 170–215（46 aa）
Chain R 170–215（46 aa）
Chain S 170–215（46 aa）
Chain T 170–215（46 aa）
Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E Mutation：A315E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7KWZ TDP-43 LCD amyloid fibrils Deposited 2020-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 151–298（148 aa）
Chain B 151–298（148 aa）
Chain C 151–298（148 aa）
Chain D 151–298（148 aa）
Chain E 151–298（148 aa）
Mutation：low complexity domain (UNP residues 151-298) Mutation：low complexity domain (UNP residues 151-298) Mutation：low complexity domain (UNP residues 151-298) Mutation：low complexity domain (UNP residues 151-298) Mutation：low complexity domain (UNP residues 151-298) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7N9H Structure of the mammalian importin a1 bound to the TDP-43 NLS Deposited 2021-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 79–102（24 aa） Fragment：Nuclear localization signal motif, residues 79-102
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.5M sodium citrate, 10 mM mercaptoethanol
Resolution 2.20 Å R-free 0.215
7PY2 Structure of pathological TDP-43 filaments from ALS with FTLD Deposited 2021-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
7Q3U Cryo-EM structure of TDP43 core peptide amyloid fiber Deposited 2021-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 279–360（82 aa）
Chain B 279–360（82 aa）
Chain C 279–360（82 aa）
Chain D 279–360（82 aa）
Chain E 279–360（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8A6I Structure of the low complexity domain of TDP-43 (fragment 309-350) with methionine sulfoxide modifications Deposited 2022-06-17 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 309–350（42 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1
NMR sample composition 500 uM [U-13C; U-15N] TDP-43 fragment 309-350, 20 mM HEPES, 10 mM potassium chloride, 5 mM MgCl2, 1 mM ATP, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8CG3 Structure of TDP-43 amyloid filament from type A FTLD-TDP (variant 1) Deposited 2023-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Chain U 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.39 Å
8CGG Structure of TDP-43 amyloid filament from type A FTLD-TDP (variant 2) Deposited 2023-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Chain U 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8CGH Structure of TDP-43 amyloid filament from type A FTLD-TDP (variant 3) Deposited 2023-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Chain U 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
8QX9 TDP-43 amyloid fibrils: Morphology-1a Deposited 2023-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Chain E 1–414（414 aa）
Chain F 1–414（414 aa）
Chain G 1–414（414 aa）
Chain H 1–414（414 aa）
Chain I 1–414（414 aa）
Chain J 1–414（414 aa）
Chain K 1–414（414 aa）
Chain L 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
8QXA TDP-43 amyloid fibrils: Morphology-1b Deposited 2023-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Chain E 1–414（414 aa）
Chain F 1–414（414 aa）
Chain G 1–414（414 aa）
Chain H 1–414（414 aa）
Chain I 1–414（414 aa）
Chain J 1–414（414 aa）
Chain K 1–414（414 aa）
Chain L 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
8QXB TDP-43 amyloid fibrils: Morphology-2 Deposited 2023-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: 18-meric
Chain A 1–414（414 aa）
Chain B 1–414（414 aa）
Chain C 1–414（414 aa）
Chain D 1–414（414 aa）
Chain E 1–414（414 aa）
Chain F 1–414（414 aa）
Chain G 1–414（414 aa）
Chain H 1–414（414 aa）
Chain I 1–414（414 aa）
Chain J 1–414（414 aa）
Chain K 1–414（414 aa）
Chain L 1–414（414 aa）
Chain M 1–414（414 aa）
Chain N 1–414（414 aa）
Chain O 1–414（414 aa）
Chain P 1–414（414 aa）
Chain Q 1–414（414 aa）
Chain R 1–414（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
9FOF Structure of heteromeric amyloid filament of TDP-43 and AXNA11 from FTLD-TDP Type C (variant 2) Deposited 2024-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 282–345（64 aa）
Chain C 282–345（64 aa）
Chain E 282–345（64 aa）
Chain G 282–345（64 aa）
Chain I 282–345（64 aa）
Chain q 282–345（64 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9FOR Structure of heteromeric amyloid filament of TDP-43 and AXNA11 from FTLD-TDP Type C (variant 1) Deposited 2024-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 284–345（62 aa）
Chain C 284–345（62 aa）
Chain E 284–345（62 aa）
Chain G 284–345（62 aa）
Chain o 284–345（62 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å

41 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TADBP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–80； UniProt 1–80 Author chain C； PDBConstruct 1–80； UniProt 1–80 Author chain E； PDBConstruct 1–80； UniProt 1–80 Author chain G； PDBConstruct 1–80； UniProt 1–80 Author chain I； PDBConstruct 1–80； UniProt 1–80

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6t4b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6t4b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6t4b
Deposition date deposition_date2019-10-13
Structure title titleCRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION
Keywords keywordsMND, NTD domain, TDP-43, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.90 Å
Radius of gyration Rg (electron density) rg_electron29.27 Å
Forward intensity I(0) i033798700.00
Molecular weight molecular_weight43402.0 kDa
Excluded volume excluded_volume53469 ų
Envelope volume envelope_volume73224 ų
Hydration-shell volume shell_volume22342 ų
Envelope diameter envelope_diameter100.4 Å
Shell Rg shell_rg34.12 Å
Envelope Rg envelope_rg28.95 Å
Shape Rg shape_rg29.25 Å
Total Rg total_rg29.79 Å
Total atoms total_atoms3045
Residues n_residues390
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax96.5 Å
Rg (real space) rg_real30.15 Å
Rg uncertainty (real space) rg_real_error0.78 Å
I(0) (real space) i0_real3.3800e+07
I(0) uncertainty (real space) i0_real_error5.5540e+05
Rg (reciprocal space) rg_reciprocal30.05 Å
I(0) (reciprocal space) i0_reciprocal33800000.0000
Solution quality estimate total_estimate0.8006
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.8 Å
Skewness Skewness skewness0.407
Kurtosis Kurtosis kurtosis-0.725
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26120000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.596; Smooth: 0.681
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)