← Back to search
1iaj

CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (APO)

Method: X-RAY DIFFRACTION Dmax: 115.7 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSIENT RECEPTOR POTENTIAL-RELATED PROTEIN

Mus musculus

UniProt Q923J1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1549–1828 Chain B； UniProt 1549–1828 Fragment：PROTEIN KINASE DOMAIN, RESIDUES 1549-1828 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；HEPES, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K Resolution 2.80 Å R-free 0.292

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 1IAJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IA9 CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (AMPPNP COMPLEX) Deposited 2001-03-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1549–1828（280 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 1549-1828
Chain B 1549–1828（280 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 1549-1828
Not recorded ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, ammonium phosphate, AMPPNP, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.294
1IAH CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (ADP-MG COMPLEX) Deposited 2001-03-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1549–1828（280 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 1549-1828
Chain B 1549–1828（280 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 1549-1828
Not recorded ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, ammonium phosphate, ADP, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.249
5ZX5 3.3 angstrom structure of mouse TRPM7 with EDTA Deposited 2018-05-18 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 × 4 PDB declaration: tetrameric
Chain A 2–1230（1229 aa）
Chain B 2–1230（1229 aa）
Chain C 2–1230（1229 aa）
Chain D 2–1230（1229 aa）
Not recorded Y01 CHOLESTEROL HEMISUCCINATE × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
8SI2 Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in apo state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 64 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å
8SI3 Cryo-EM structure of TRPM7 in GDN detergent in apo state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
8SI4 Cryo-EM structure of TRPM7 N1098Q mutant in GDN detergent in open state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Mutation：N1098Q Mutation：N1098Q Mutation：N1098Q Mutation：N1098Q POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 8 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8SI5 Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in complex with agonist naltriben in open state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 ZY8 (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,9,14b-hexahydro-8aH-4,8-methanobis[1]benzofuro[3,2-e:2',3'-g]isoquinoline-1,8a-diol × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.17 Å
8SI6 Cryo-EM structure of TRPM7 in MSP2N2 nanodisc in complex with agonist naltriben in closed state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 ZY8 (4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,9,14b-hexahydro-8aH-4,8-methanobis[1]benzofuro[3,2-e:2',3'-g]isoquinoline-1,8a-diol × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
8SI7 Cryo-EM structure of TRPM7 in GDN detergent in complex with inhibitor VER155008 in closed state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 3FD 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile × 4 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
8SI8 Cryo-EM structure of TRPM7 N1098Q mutant in GDN detergent in complex with inhibitor VER155008 in closed state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Mutation：N1098Q Mutation：N1098Q Mutation：N1098Q Mutation：N1098Q POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 3FD 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile × 4 CLR CHOLESTEROL × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
8SIA Cryo-EM structure of TRPM7 N1098Q mutant in GDN detergent in complex with inhibitor NS8593 in closed state Deposited 2023-04-14 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 × 4 PDB declaration: tetrameric
Chain A 2–1280（1279 aa）
Chain B 2–1280（1279 aa）
Chain C 2–1280（1279 aa）
Chain D 2–1280（1279 aa）
Mutation：N1098Q Mutation：N1098Q Mutation：N1098Q Mutation：N1098Q POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 6RA N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]-1H-benzimidazol-2-amine × 4 CA CALCIUM ION × 1 CLR CHOLESTEROL × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8SIB Cryo-EM structure of TRPM7 MHR1-3 domain Deposited 2023-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–1280（1279 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8W2L TRPM7 structure in complex with anticancer agent CCT128930 in closed state Deposited 2024-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 3–1280（1278 aa） Fragment：residues 3-1280 of the TRPM7 channel
Chain B 3–1280（1278 aa） Fragment：residues 3-1280 of the TRPM7 channel
Chain C 3–1280（1278 aa） Fragment：residues 3-1280 of the TRPM7 channel
Chain D 3–1280（1278 aa） Fragment：residues 3-1280 of the TRPM7 channel
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 52 CLR CHOLESTEROL × 4 M05 4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium × 4 DU0 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPM7_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–280； UniProt 1549–1828 Author chain B； PDBConstruct 1–280； UniProt 1549–1828

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 1iaj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1iaj
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1iaj
Deposition date deposition_date2001-03-22
Structure title titleCRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (APO)
Keywords keywordsalpha/beta, protein kinase like fold, ATP-grasp fold, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.58 Å
Radius of gyration Rg (electron density) rg_electron33.25 Å
Forward intensity I(0) i054895800.00
Molecular weight molecular_weight58868.0 kDa
Excluded volume excluded_volume73693 ų
Envelope volume envelope_volume94978 ų
Hydration-shell volume shell_volume26033 ų
Envelope diameter envelope_diameter122.3 Å
Shell Rg shell_rg36.45 Å
Envelope Rg envelope_rg32.99 Å
Shape Rg shape_rg33.23 Å
Total Rg total_rg33.58 Å
Total atoms total_atoms4134
Residues n_residues512
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.7 Å
Rg (real space) rg_real33.96 Å
Rg uncertainty (real space) rg_real_error1.18 Å
I(0) (real space) i0_real5.4900e+07
I(0) uncertainty (real space) i0_real_error9.9330e+05
Rg (reciprocal space) rg_reciprocal33.73 Å
I(0) (reciprocal space) i0_reciprocal54880000.0000
Solution quality estimate total_estimate0.7228
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.504
Kurtosis Kurtosis kurtosis-0.669
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11760000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.427; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.240; Smooth: 0.870
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1iaja_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.5 — MHCK/EF2 kinase
Domain ID domain_idd1iajb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.5 — MHCK/EF2 kinase

CATH v4.4 (4 domains)

Domain ID domain_id1iajA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id1iajA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology200 — Protein kinase-like fold
Homologous superfamily homologous superfamily10 — MHCK/EF2 kinase
Domain ID domain_id1iajB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id1iajB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology200 — Protein kinase-like fold
Homologous superfamily homologous superfamily10 — MHCK/EF2 kinase
▶

8. Citations (1)

▶

9. Files and Curves (10)