Segment of TAR DNA-binding protein 43
OrganismNot specified
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 homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count | Chain A; UniProt 312–317 | Fragment:UNP residues 312-317 Mutation:A315T | No other associated polymer | 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 |
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 5WHP | 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 mutation/modification 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 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 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 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 mutation/modification Different oligomeric state 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 |
| 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 mutation/modification 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 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 mutation/modification 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 mutation/modification 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 oligomeric state 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 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 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 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 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 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 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 |
| 6T4B CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION Deposited 2019-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
1–80(80 aa)
|
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 |
| 6T4B CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION Deposited 2019-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain C
1–80(80 aa)
|
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 |
| 6T4B CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION Deposited 2019-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain E
1–80(80 aa)
|
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 |
| 6T4B CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION Deposited 2019-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain G
1–80(80 aa)
|
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 |
| 6T4B CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION Deposited 2019-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain I
1–80(80 aa)
|
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 |
| 7KWZ TDP-43 LCD amyloid fibrils Deposited 2020-12-02 | Different construct Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 51 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 1–6; UniProt 312–317 |