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- PDB-3mjh: Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Fi... -

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Basic information

Entry
Database: PDB / ID: 3mjh
TitleCrystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1
Components
  • Early endosome antigen 1
  • Ras-related protein Rab-5A
KeywordsPROTEIN TRANSPORT / PROTEIN-ZINC FINGER COMPLEX / BETA BETA ALPHA FOLD / BETA HAIRPIN / Rab5A GTPase / EEA1
Function / homology
Function and homology information


serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / synaptic vesicle recycling / axonal spine / amyloid-beta clearance by transcytosis ...serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / synaptic vesicle recycling / axonal spine / amyloid-beta clearance by transcytosis / chemical synaptic transmission, postsynaptic / vesicle fusion / modulation by host of viral process / regulation of autophagosome assembly / GTP-dependent protein binding / regulation of filopodium assembly / RAB geranylgeranylation / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / canonical Wnt signaling pathway / endomembrane system / phagocytic vesicle / axon terminus / phagocytosis / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / ruffle / small monomeric GTPase / G protein activity / clathrin-coated endocytic vesicle membrane / regulation of long-term neuronal synaptic plasticity / intracellular protein transport / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / recycling endosome / endocytosis / phagocytic vesicle membrane / GDP binding / melanosome / synaptic vesicle / actin cytoskeleton / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / postsynapse / early endosome / calmodulin binding / endosome membrane / endosome / membrane raft / axon / intracellular membrane-bounded organelle / GTPase activity / dendrite / neuronal cell body / glutamatergic synapse / GTP binding / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Zinc finger, FYVE/PHD-type / Small GTP-binding protein domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-5A / Early endosome antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMishra, A.K. / Eathiraj, S. / Lambright, D.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1).
Authors: Mishra, A. / Eathiraj, S. / Corvera, S. / Lambright, D.G.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-5A
B: Early endosome antigen 1
C: Ras-related protein Rab-5A
D: Early endosome antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,18510
Polymers44,9594
Non-polymers1,2266
Water5,621312
1
A: Ras-related protein Rab-5A
B: Early endosome antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0925
Polymers22,4792
Non-polymers6133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area9870 Å2
MethodPISA
2
C: Ras-related protein Rab-5A
D: Early endosome antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0925
Polymers22,4792
Non-polymers6133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.412, 80.398, 103.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein Ras-related protein Rab-5A


Mass: 18801.445 Da / Num. of mol.: 2 / Fragment: residues 16-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5, RAB5A / Plasmid: modified pET15b, modified pET28a,pGEX / Production host: Escherichia coli (E. coli)
Strain (production host): K12, BL21 (DE3)Codon Plus RIL cells
References: UniProt: P20339, small monomeric GTPase
#2: Protein/peptide Early endosome antigen 1 / Endosome-associated protein p162 / Zinc finger FYVE domain-containing protein 2


Mass: 3678.005 Da / Num. of mol.: 2 / Fragment: C2H2-type, residues 36-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Early Endosomal Antigen1(EEA1), EEA1, ZFYVE2 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli)
Strain (production host): K12, BL21(DE3)Codon Plus RIL cells
References: UniProt: Q15075

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Non-polymers , 4 types, 318 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2007 / Details: mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 27931 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 35.344 Å2 / Rsym value: 0.042 / Net I/σ(I): 44.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.3.0037refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mouse Rab5C

Resolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.351 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.275 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25989 1157 5 %RANDOM
Rwork0.19229 ---
all0.195 21886 --
obs0.19568 21886 89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.193 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2---1.26 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 68 312 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223253
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9694404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65225.168149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68415555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8151512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022416
X-RAY DIFFRACTIONr_nbd_refined0.2030.21534
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2261
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.221
X-RAY DIFFRACTIONr_mcbond_it0.6081.52046
X-RAY DIFFRACTIONr_mcangle_it1.03723184
X-RAY DIFFRACTIONr_scbond_it1.41731389
X-RAY DIFFRACTIONr_scangle_it2.2134.51220
LS refinement shellResolution: 2.025→2.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 68 -
Rwork0.242 1174 -
obs--67.1 %

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