3tnf

LidA from Legionella in complex with active Rab8a

Method: X-RAY DIFFRACTION D_max: 112.1 Å Quality: GOOD

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

Ras-related protein Rab-8A

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 6–176	Fragment：unp residues 6-176	LidA × 1 （Q5ZWZ3） MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；50% (v/v) MPD , 0.1 M sodium cacodylate pH 5.6, 10 mM spermidine, vapor diffusion, hanging drop, temperature 293K	Resolution 2.50 Å R-free 0.275

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 3TNF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	Resolution 2.00 Å R-free 0.241
4LHV Crystal structure of Rab8 in its inactive GDP-bound form Deposited 2013-07-01	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 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form Deposited 2013-07-01	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 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form Deposited 2013-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form Deposited 2013-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form Deposited 2013-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.244
4LHW Crystal structure of Rab8 in its active GppNHp-bound form Deposited 2013-07-01	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 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form Deposited 2013-07-01	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 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form Deposited 2013-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form Deposited 2013-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form Deposited 2013-07-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 6–176（171 aa） Fragment：unp residues 6-176	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.183
4LHX Crystal structure of nucleotide-free Rab8:Rabin8 Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES. cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES), pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.300
4LHX Crystal structure of nucleotide-free Rab8:Rabin8 Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES. cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES), pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.300
4LHY Crystal structure of GDP-bound Rab8:Rabin8 Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.310
4LHY Crystal structure of GDP-bound Rab8:Rabin8 Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.310
4LHZ Crystal structure of GTP-bound Rab8:Rabin8 Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hours at 278 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.309
4LHZ Crystal structure of GTP-bound Rab8:Rabin8 Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hours at 278 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.309
4LI0 Crystal structure of GDP-bound Rab8:GRAB Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1.6 M ammonium sulphate and sodium acetate. cryo solution containing 20% glycerol in the reservoir solution, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.290
4LI0 Crystal structure of GDP-bound Rab8:GRAB Deposited 2013-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–184（184 aa） Fragment：unp residues 1-184	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1.6 M ammonium sulphate and sodium acetate. cryo solution containing 20% glycerol in the reservoir solution, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.290
5SZI Structure of human Rab8a in complex with the bMERB domain of Mical-cL Deposited 2016-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–207（207 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M bis tris propane 0.2M tri sodium citrate 20% PEG 3350	Resolution 2.85 Å R-free 0.288
6RIR Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2 Deposited 2019-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–181（181 aa） Chain B 1–181（181 aa）	Mutation：Q67L Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q67L Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；8% PEG 8K 100mM Na HEPES	Resolution 1.77 Å R-free 0.210
6SQ2 Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2 Deposited 2019-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–181（181 aa） Chain B 1–181（181 aa）	Mutation：Q67L, T72E Mutation：Q67L, T72E	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；100mM HEPES 10% PEG 4,000 10% 2-propanol	Resolution 1.68 Å R-free 0.202
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP Deposited 2019-09-10	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 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	Resolution 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP Deposited 2019-09-10	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 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	Resolution 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP Deposited 2019-09-10	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 C 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	Resolution 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP Deposited 2019-09-10	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 D 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	Resolution 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP Deposited 2019-09-10	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 E 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	Resolution 2.40 Å R-free 0.262
6STG Human Rab8a phosphorylated at Ser111 in complex with GPPNP Deposited 2019-09-10	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 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 30% PEG300	Resolution 2.50 Å R-free 0.278
6STG Human Rab8a phosphorylated at Ser111 in complex with GPPNP Deposited 2019-09-10	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 6–176（171 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 30% PEG300	Resolution 2.50 Å R-free 0.278
6WHE Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state Deposited 2020-04-08	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 1–181（181 aa）	Mutation：Q67L/T72E	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；20% PEG3350, 0.1M Hepes pH 7	Resolution 1.73 Å R-free 0.230
6WHE Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state Deposited 2020-04-08	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 1–181（181 aa）	Mutation：Q67L/T72E	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；20% PEG3350, 0.1M Hepes pH 7	Resolution 1.73 Å R-free 0.230
6ZSI The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–176（176 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6.0 5% w/v PEG 3000 30% v/v PEG 200	Resolution 1.91 Å R-free 0.267
6ZSI The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–176（176 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6.0 5% w/v PEG 3000 30% v/v PEG 200	Resolution 1.91 Å R-free 0.267
6ZSJ The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–176（176 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol	Resolution 2.00 Å R-free 0.291
6ZSJ The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–176（176 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol	Resolution 2.00 Å R-free 0.291
7BWT SopD-Rab8 complex structure Deposited 2020-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–183（182 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 9 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.05M Sodium cacodylate trihydrate pH 6.5, 0.2 M MgCl2, 11.5% PEG4000	Resolution 2.30 Å R-free 0.215
7LWB Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2 Deposited 2021-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–181（181 aa）	Mutation：Q67L Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；288 K；150mM DL-Malic acid, 20% PEG3350	Resolution 1.90 Å R-free 0.267
9IKQ Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L) Deposited 2024-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–181（181 aa） Chain B 1–181（181 aa）	Mutation：Q67L Mutation：Q67L	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000	Resolution 1.93 Å R-free 0.218
9M0O Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L) Deposited 2025-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–176（176 aa）	Mutation：Q67L	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GOL GLYCEROL × 6 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05 M Imidazole pH 6.5, 0.5 M Sodium acetate trihydrate	Resolution 1.83 Å R-free 0.222

19 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAB8A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–174； UniProt 6–176

LidA

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

UniProt Q5ZWZ3

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 B； UniProt 201–583	Fragment：unp residues 201-583	Ras-related protein Rab-8A × 1 （P61006） MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；50% (v/v) MPD , 0.1 M sodium cacodylate pH 5.6, 10 mM spermidine, vapor diffusion, hanging drop, temperature 293K	Resolution 2.50 Å R-free 0.275

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q5ZWZ3_LEGPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–384； UniProt 201–583

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	3tnf
Deposition date deposition_date	2011-09-01
Structure title title	LidA from Legionella in complex with active Rab8a
Keywords keywords	;Protein transport, vesicular trafficking, GTPase, Legionella pneumophila, Rab8a, vesicle recuitment, LCV, DrrA, SidM, Rab-effector, vesicular transport, GDP/GTP binding Rab-binding, ER, Golgi, Plasmamembrane ;; PROTEIN TRANSPORT
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	28.65 Å
Radius of gyration Rg (electron density) rg_electron	28.09 Å
Forward intensity I(0) i0	68820900.00
Molecular weight molecular_weight	64426.0 kDa
Excluded volume excluded_volume	80545 Å³
Envelope volume envelope_volume	105130 Å³
Hydration-shell volume shell_volume	32612 Å³
Envelope diameter envelope_diameter	118.3 Å
Shell Rg shell_rg	33.71 Å
Envelope Rg envelope_rg	28.71 Å
Shape Rg shape_rg	28.12 Å
Total Rg total_rg	28.58 Å
Total atoms total_atoms	4528
Residues n_residues	549
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	112.1 Å
Rg (real space) rg_real	28.77 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	6.8820e+07
I(0) uncertainty (real space) i0_real_error	1.2340e+06
Rg (reciprocal space) rg_reciprocal	28.72 Å
I(0) (reciprocal space) i0_reciprocal	68820000.0000
Solution quality estimate total_estimate	0.7826
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.594
Kurtosis Kurtosis kurtosis	0.450
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9146000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.484; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.738; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rab-8A
Molecular weight formula_weight	20012.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4590

GHMDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKK

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	LidA
Molecular weight formula_weight	44637.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GMLDEYEQAIKRAQENIKKGEELEKKLDKLERQGKDLEDKYKTYEENLEGFEKLLTDSEELSLSEINEKMEAFSKDSEKLTQLMEKHKGDEKTVQSLQREHHDIKAKLANLQVLHDAHTGKKSYVNEKGNPVSSLKDAHLAINKDQEVVEHEGQFYLLQKGQWDAIKNNPAALEKAQKDYSQSKHDLATIKMEALIHKLSLEMEKQLETINNLIMSTDPKENEEATKLLHKHNGLNLKLANLQDMLAVHRKEKSFFNEKGEEVTSLNDAHYVIGKDQQLFNLGGKFYPIHKEQKILEKDGKFYLLKQGEDWESIKDSPEKQKKAEHDFHKLQYETPMTVKKLVHHNKGLETTIHKERVEETKQQLEDNGKEKIEIANNISKLQS

来源 Source

来源生物 organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3tnfa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (3 domains)

Domain ID domain_id	3tnfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3tnfB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	390 —

Domain ID domain_id	3tnfB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	2010 —

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8. Citations (1)

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Unit-cell length a length_a	103.820 Å
Unit-cell length b length_b	103.820 Å
Unit-cell length c length_c	150.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2189
R_work r_work	0.2160
R_free r_free	0.2747

fit	/app/data/saxs_computation/tn/3tnf/3tnf.fit
pddf	/app/data/pr_computation/tn/3tnf/3tnf.pr.out
profile	/app/data/saxs_computation/tn/3tnf/3tnf.dat

LidA from Legionella in complex with active Rab8a

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

Ras-related protein Rab-8A

State in the Current Structure

Other States of the Same Protein in the Database

LidA

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)