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7pqe

Structure of SidJ/CaM bound to SdeA in post-catalysis state

Method: ELECTRON MICROSCOPY Dmax: 122.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitinating/deubiquitinating enzyme SdeA

Legionella pneumophila

UniProt Q5ZTK4

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 231–1190 Not recorded Calmodulin-dependent glutamylase SidJ × 1 （Q5ZTK6） Calmodulin × 1 （P0DP24） MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7PQE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14 Different construct 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 756–905（150 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.06 Å R-free 0.269
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 756–905（150 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.06 Å R-free 0.269
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 756–905（150 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.06 Å R-free 0.269
5YSJ SdeA mART-C domain WT apo Deposited 2017-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 756–905（150 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.06 Å R-free 0.269
5YSK SdeA mART-C domain EE/AA apo Deposited 2017-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 756–905（150 aa）
Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.40 Å R-free 0.261
5YSK SdeA mART-C domain EE/AA apo Deposited 2017-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 756–905（150 aa）
Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.40 Å R-free 0.261
5YSK SdeA mART-C domain EE/AA apo Deposited 2017-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 756–905（150 aa）
Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.40 Å R-free 0.261
5YSK SdeA mART-C domain EE/AA apo Deposited 2017-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 756–905（150 aa）
Mutation：E860A, E862A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG400, Tris
Resolution 2.40 Å R-free 0.261
6G0C Crystal structure of SdeA catalytic core Deposited 2018-03-17 Different construct 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 213–907（695 aa）
Not recorded 1PS 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；300 K；100mM Bis Tris Propane pH 7.0-8.0, 0.1-0.2M sodium citrate tribasic dihydrate, 20-30% PEG 3350
Resolution 2.80 Å R-free 0.293
6WTG SdeA DUB Domain in complex with Ubiquitin Deposited 2020-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–193（193 aa）
Mutation：C118A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.1 M bicine pH 9.0, 65% (v/v) MPD
Resolution 2.63 Å R-free 0.243
7MIR Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex Deposited 2021-04-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 231–1190（960 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7PPO Structure of SidJ/CaM bound to SdeA in pre-glutamylation state Deposited 2021-09-14 Different mutation/modification Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 231–1190（960 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
9R3T C-terminal domain of SdeA Legionella effector Deposited 2025-05-06 Different construct 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 1158–1499（342 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium chloride, 0.1 M sodium/ potassium phosphate pH-7.5, 50% PEG 200
Resolution 1.98 Å R-free 0.250
9R3T C-terminal domain of SdeA Legionella effector Deposited 2025-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1158–1499（342 aa）
Not recorded EDO 1,2-ETHANEDIOL × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium chloride, 0.1 M sodium/ potassium phosphate pH-7.5, 50% PEG 200
Resolution 1.98 Å R-free 0.250

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SDEA_LEGPH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–979； UniProt 231–1190

Calmodulin-dependent glutamylase SidJ

Legionella pneumophila

UniProt Q5ZTK6

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 99–873 Mutation：E565A Ubiquitinating/deubiquitinating enzyme SdeA × 1 （Q5ZTK4） Calmodulin × 1 （P0DP24） MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7PQE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6K4K Crystal structure of SidJ-CaM binary complex at 2.71 A Deposited 2019-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–873（873 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；299 K；20% PEG 3350, 0.2M NaI
Resolution 2.71 Å R-free 0.243
6K4K Crystal structure of SidJ-CaM binary complex at 2.71 A Deposited 2019-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–873（873 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；299 K；20% PEG 3350, 0.2M NaI
Resolution 2.71 Å R-free 0.243
6K4L Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A Deposited 2019-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–873（873 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI
Resolution 2.95 Å R-free 0.269
6K4L Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A Deposited 2019-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–873（873 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI
Resolution 2.95 Å R-free 0.269
6K4R Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A Deposited 2019-05-26 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 × 2 PDB declaration: dimeric
Chain A 1–873（873 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 CL CHLORIDE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI, 0.1M HEPES 7.5
Resolution 3.11 Å R-free 0.279
6K4R Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A Deposited 2019-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–873（873 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI, 0.1M HEPES 7.5
Resolution 3.11 Å R-free 0.279
6OQQ Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex Deposited 2019-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–873（873 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 4 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 9 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M sodium malonate, 0.01 M sodium chloride, 0.001 M magnesium chloride, 0.001 mM calcium chloride, 0.001 M AMP-CPP, 16-17% PEG 3350, 35-40% ethylene glycol
Resolution 2.10 Å R-free 0.234
6OQQ Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex Deposited 2019-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–873（873 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 2 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M sodium malonate, 0.01 M sodium chloride, 0.001 M magnesium chloride, 0.001 mM calcium chloride, 0.001 M AMP-CPP, 16-17% PEG 3350, 35-40% ethylene glycol
Resolution 2.10 Å R-free 0.234
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01 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 × 2 PDB declaration: dimeric
Chain A 97–853（757 aa）
Not recorded CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP
Resolution 2.59 Å R-free 0.241
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 97–853（757 aa）
Not recorded CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP
Resolution 2.59 Å R-free 0.241
6S5T Legionella pneumophila SidJ-Human calmodulin complex Deposited 2019-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–873（873 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.15 Å
7MIR Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex Deposited 2021-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 97–851（755 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7MIS Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex Deposited 2021-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 97–851（755 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CA CALCIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7PPO Structure of SidJ/CaM bound to SdeA in pre-glutamylation state Deposited 2021-09-14 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 99–873（775 aa）
Mutation：E565A MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SIDJ_LEGPH
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 19–793； UniProt 99–873

Calmodulin

Homo sapiens

UniProt P0DP24

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–149 Not recorded Ubiquitinating/deubiquitinating enzyme SdeA × 1 （Q5ZTK4） Calmodulin-dependent glutamylase SidJ × 1 （Q5ZTK6） MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 7PQE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–148（147 aa）
Not recorded CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP
Resolution 2.59 Å R-free 0.241
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–148（147 aa）
Not recorded CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP
Resolution 2.59 Å R-free 0.241
6S5T Legionella pneumophila SidJ-Human calmodulin complex Deposited 2019-07-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–149（149 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.15 Å
6SZ5 Human calmodulin bound to a peptide of human NADPH oxidase 5 Deposited 2019-10-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–149（149 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30 mM Tris-HCl at pH 7.4, 2.5 mM CaCl2 and 2.5% (v/v) glycerol
Resolution 2.23 Å R-free 0.294
6XXF 1.7 Angstrom crystal structure of Ca/CaM:RyR2 peptide complex Deposited 2020-01-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain AAA 1–149（149 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium acetate pH4.5, 0.2M ammonium acetate, 10% PEG4000
Resolution 1.70 Å R-free 0.205
6Y4O Calmodulin bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain Deposited 2020-02-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–149（149 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M Sodium Acetate pH 4.70 and 23 % PEG 550 MME
Resolution 1.84 Å R-free 0.208
7MIR Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex Deposited 2021-04-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–149（149 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7MIS Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex Deposited 2021-04-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–149（149 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CA CALCIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7PPO Structure of SidJ/CaM bound to SdeA in pre-glutamylation state Deposited 2021-09-14 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–149（149 aa）
Not recorded MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8K9Z Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–149（149 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG 3350 and 0.18 M magnesium acetate
Resolution 2.90 Å R-free 0.304
8K9Z Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–149（149 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG 3350 and 0.18 M magnesium acetate
Resolution 2.90 Å R-free 0.304
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–149（149 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking
Resolution 2.35 Å R-free 0.263
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–149（149 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking
Resolution 2.35 Å R-free 0.263
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–149（149 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking
Resolution 2.35 Å R-free 0.263
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–149（149 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking
Resolution 2.35 Å R-free 0.263
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02 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 × 2 PDB declaration: dimeric
Chain B 1–149（149 aa）
Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2
Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–149（149 aa）
Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2
Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–149（149 aa）
Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2
Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–149（149 aa）
Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2
Resolution 2.82 Å R-free 0.342

11 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 20–168； UniProt 1–149

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 7pqe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7pqe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7pqe
Deposition date deposition_date2021-09-17
Structure title titleStructure of SidJ/CaM bound to SdeA in post-catalysis state
Keywords keywordsGlutamylase, Pseudokinase, phosphoribosyl, ubiquitination, Complex, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.39 Å
Radius of gyration Rg (electron density) rg_electron35.67 Å
Forward intensity I(0) i0351046000.00
Molecular weight molecular_weight152380.0 kDa
Excluded volume excluded_volume191000 ų
Envelope volume envelope_volume249600 ų
Hydration-shell volume shell_volume56970 ų
Envelope diameter envelope_diameter131.3 Å
Shell Rg shell_rg42.76 Å
Envelope Rg envelope_rg36.11 Å
Shape Rg shape_rg35.65 Å
Total Rg total_rg36.20 Å
Total atoms total_atoms10745
Residues n_residues1364
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 dmax122.4 Å
Rg (real space) rg_real36.36 Å
Rg uncertainty (real space) rg_real_error1.06 Å
I(0) (real space) i0_real3.5100e+08
I(0) uncertainty (real space) i0_real_error5.8620e+06
Rg (reciprocal space) rg_reciprocal36.38 Å
I(0) (reciprocal space) i0_reciprocal351100000.0000
Solution quality estimate total_estimate0.8610
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.7 Å
Skewness Skewness skewness0.369
Kurtosis Kurtosis kurtosis-0.177
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha64800000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.723
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (2)

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9. Files and Curves (10)