3iec

Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates

Method: X-RAY DIFFRACTION D_max: 141.2 Å Quality: GOOD

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

Serine/threonine-protein kinase MARK2

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 49–363	Fragment：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 49–363	Fragment：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 49–363	Fragment：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 49–363	Fragment：UNP RESIDUES 49-363	Cytotoxicity-associated immunodominant antigen × 1 （P55980）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248

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 3IEC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties Deposited 2015-10-16	Different construct 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 39–364（326 aa） Fragment：CATALYTIC DOMAIN (UNP RESIDUES 39-364)	Not recorded	24R N-[(1S,2R)-2-aminocyclohexyl]-4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE	Resolution 2.80 Å R-free 0.254
5EAK Optimization of Microtubule Affinity Regulating Kinase (MARK) Inhibitors with Improved Physical Properties Deposited 2015-10-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 39–364（326 aa） Fragment：CATALYTIC DOMAIN (UNP RESIDUES 39-364)	Not recorded	24R N-[(1S,2R)-2-aminocyclohexyl]-4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE	Resolution 2.80 Å R-free 0.254
5KZ7 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23	Different construct 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 6–331（326 aa） Fragment：UNP residues 6-331	Not recorded	6Z2 7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE	Resolution 3.20 Å R-free 0.293
5KZ7 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 6–331（326 aa） Fragment：UNP residues 6-331	Not recorded	6Z2 7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE	Resolution 3.20 Å R-free 0.293
5KZ8 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23	Different construct 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 6–331（326 aa） Fragment：UNP residues 6-331	Not recorded	6Z5 5,5-dimethyl-7-[(1~{S})-4-oxidanyl-1~{H}-inden-1-yl]-2-phenylazanyl-pyrrolo[2,3-d]pyrimidin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE	Resolution 3.21 Å R-free 0.290
5KZ8 Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one Deposited 2016-07-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 6–331（326 aa） Fragment：UNP residues 6-331	Not recorded	6Z5 5,5-dimethyl-7-[(1~{S})-4-oxidanyl-1~{H}-inden-1-yl]-2-phenylazanyl-pyrrolo[2,3-d]pyrimidin-6-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS PH 6.5, 14% PEG3350, 200MM AMM.SULFATE	Resolution 3.21 Å R-free 0.290
8TXY X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera Deposited 2023-08-24	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 47–363（317 aa）	Mutation：I59L, K66V V81I, L97I, V113I, M129T, S133K, G134N , S197G	PEG DI(HYDROXYETHYL)ETHER × 2 SJ0 N-[(5P,8R)-5-(2-cyano-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}pyridin-4-yl)pyrazolo[1,5-a]pyridin-2-yl]cyclopropanecarboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；298 K；24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8	Resolution 2.10 Å R-free 0.267
8TXY X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera Deposited 2023-08-24	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 B 47–363（317 aa）	Mutation：I59L, K66V V81I, L97I, V113I, M129T, S133K, G134N , S197G	PEG DI(HYDROXYETHYL)ETHER × 1 SJ0 N-[(5P,8R)-5-(2-cyano-5-{[(3R)-1-methylpyrrolidin-3-yl]methoxy}pyridin-4-yl)pyrazolo[1,5-a]pyridin-2-yl]cyclopropanecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；298 K；24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8	Resolution 2.10 Å R-free 0.267

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MARK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–319； UniProt 49–363 Author chain B； PDBConstruct 5–319； UniProt 49–363 Author chain C； PDBConstruct 5–319； UniProt 49–363 Author chain D； PDBConstruct 5–319； UniProt 49–363

Cytotoxicity-associated immunodominant antigen

Helicobacter pylori

UniProt P55980

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 885–1005	Fragment：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 885–1005	Fragment：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 885–1005	Fragment：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 885–1005	Fragment：UNP RESIDUES 885-1005	Serine/threonine-protein kinase MARK2 × 1 （Q7KZI7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.248

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3IEC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DVY Crystal structure of the Helicobacter pylori CagA oncoprotein Deposited 2012-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 1–876（876 aa） Fragment：UNP residues 1-876	Mutation：H131M/L274M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；8% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.248
4DVZ Crystal structure of the Helicobacter pylori CagA oncoprotein Deposited 2012-02-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 261–829（569 aa） Fragment：UNP residues 261-829	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；7% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.19 Å R-free 0.279
4G0H Crystal structure of the N-terminal domain of Helicobacter pylori CagA protein Deposited 2012-07-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–884（884 aa） Fragment：UNP residues 1 to 884	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% Ethanol, Na Cacodylate 100mM pH7, NaI 15mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.341
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 Deposited 2013-01-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 19–235（217 aa）	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, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	Resolution 2.04 Å R-free 0.234
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 Deposited 2013-01-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–235（217 aa）	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, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	Resolution 2.04 Å R-free 0.234
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 Deposited 2013-01-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 19–235（217 aa）	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, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	Resolution 2.04 Å R-free 0.234
4IRV Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 Deposited 2013-01-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 19–235（217 aa）	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, HANGING DROP；pH 8.5；Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP	Resolution 2.04 Å R-free 0.234

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

View Construct and Data Evidence

UniProt name	CAGA_HELPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 5–125； UniProt 885–1005 Author chain F； PDBConstruct 5–125； UniProt 885–1005 Author chain G； PDBConstruct 5–125； UniProt 885–1005 Author chain H； PDBConstruct 5–125； UniProt 885–1005

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3iec
Deposition date deposition_date	2009-07-22
Structure title title	Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates
Keywords keywords	;Protein-protein complex, kinase, virulence factor, Alternative promoter usage, ATP-binding, Cell membrane, Developmental protein, Differentiation, Magnesium, Membrane, Metal-binding, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transferase, SIGNALING PROTEIN-TOXIN COMPLEX ;; SIGNALING PROTEIN/TOXIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	42.52 Å
Radius of gyration Rg (electron density) rg_electron	42.24 Å
Forward intensity I(0) i0	313534000.00
Molecular weight molecular_weight	150820.0 kDa
Excluded volume excluded_volume	191340 Å³
Envelope volume envelope_volume	264850 Å³
Hydration-shell volume shell_volume	53182 Å³
Envelope diameter envelope_diameter	145.5 Å
Shell Rg shell_rg	46.55 Å
Envelope Rg envelope_rg	41.41 Å
Shape Rg shape_rg	42.22 Å
Total Rg total_rg	42.54 Å
Total atoms total_atoms	10625
Residues n_residues	1302
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	141.2 Å
Rg (real space) rg_real	42.52 Å
Rg uncertainty (real space) rg_real_error	1.26 Å
I(0) (real space) i0_real	3.1350e+08
I(0) uncertainty (real space) i0_real_error	5.7950e+06
Rg (reciprocal space) rg_reciprocal	42.52 Å
I(0) (reciprocal space) i0_reciprocal	313500000.0000
Solution quality estimate total_estimate	0.8886
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.3 Å
Skewness Skewness skewness	0.247
Kurtosis Kurtosis kurtosis	-0.538
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44800000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.833

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Serine/threonine-protein kinase MARK2
Molecular weight formula_weight	36919.8 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11312

MADLHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGWMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGY

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytotoxicity-associated immunodominant antigen
Molecular weight formula_weight	13423.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GPVDNNNNNGLKNSTEPIYAKVNKKKTGQVASPEEPIYTQVAKKVNAKIDRLNQIASGLGGVGQAAGFPLKRHDKVDDLSKVGLSASPEPIYATIDDLGGPFPLKRHDKVDDLSKVGRSRNQELA

来源 Source

来源生物 organism	Helicobacter pylori
通用名 common_name	Campylobacter pylori
NCBI Class编号 ncbi_taxonomy_id	210
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	687

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ieca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3iecb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3iecc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d3iecd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3iecA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3iecA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3iecA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	3iecB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3iecB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3iecB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	3iecC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3iecC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3iecC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	3iecD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3iecD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3iecD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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8. Citations (1)

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Unit-cell length a length_a	93.466 Å
Unit-cell length b length_b	93.256 Å
Unit-cell length c length_c	113.955 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	40.960 Å
R factor r_factor	0.2060
R_work r_work	0.2040
R_free r_free	0.2480

fit	/app/data/saxs_computation/ie/3iec/3iec.fit
pddf	/app/data/pr_computation/ie/3iec/3iec.pr.out
profile	/app/data/saxs_computation/ie/3iec/3iec.dat

Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates

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

Serine/threonine-protein kinase MARK2

State in the Current Structure

Other States of the Same Protein in the Database

Cytotoxicity-associated immunodominant antigen

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)