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- PDB-2e6v: Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man3Gl... -

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Basic information

Entry
Database: PDB / ID: 2e6v
TitleCrystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man3GlcNAc-bound form
ComponentsVesicular integral-membrane protein VIP36
KeywordsPROTEIN TRANSPORT / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR
Function / homology
Function and homology information


COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-coated ER to Golgi transport vesicle / mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of phagocytosis ...COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-coated ER to Golgi transport vesicle / mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of phagocytosis / heat shock protein binding / protein transport / cytoplasmic vesicle / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
VIP36, lectin domain / Legume-like lectin / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Vesicular integral-membrane protein VIP36
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSatoh, T. / Kato, R. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36
Authors: Satoh, T. / Cowieson, N.P. / Hakamata, W. / Ideo, H. / Fukushima, K. / Kurihara, M. / Kato, R. / Yamashita, K. / Wakatsuki, S.
History
DepositionJan 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicular integral-membrane protein VIP36
B: Vesicular integral-membrane protein VIP36
C: Vesicular integral-membrane protein VIP36
D: Vesicular integral-membrane protein VIP36
E: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,04613
Polymers144,6575
Non-polymers1,3898
Water1,18966
1
A: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4763
Polymers28,9311
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4763
Polymers28,9311
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1523
Polymers28,9311
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9712
Polymers28,9311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Vesicular integral-membrane protein VIP36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9712
Polymers28,9311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.200, 151.200, 177.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Vesicular integral-membrane protein VIP36 / Lectin / mannose-binding 2


Mass: 28931.318 Da / Num. of mol.: 5 / Fragment: RESIDUES 51-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: LMAN2 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49256
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG4000, 0.4M Imidazole malate (pH6.0), 3.4mM Man3GlcNAc, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 54228 / Num. obs: 54152 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 5.8 / Num. unique all: 5317 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DUR

2dur


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.876 / SU B: 9.34 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.503 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2743 5.1 %RANDOM
Rwork0.221 ---
all0.224 51251 --
obs0.224 51251 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2--1.77 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9617 0 85 66 9768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0219976
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.93413538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81251161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55323.626513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0071564
X-RAY DIFFRACTIONr_chiral_restr0.0950.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027655
X-RAY DIFFRACTIONr_nbd_refined0.2090.23779
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2399
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.23
X-RAY DIFFRACTIONr_mcbond_it0.8321.55979
X-RAY DIFFRACTIONr_mcangle_it1.44629461
X-RAY DIFFRACTIONr_scbond_it1.8234585
X-RAY DIFFRACTIONr_scangle_it2.8514.54077
LS refinement shellHighest resolution: 2.5 Å / Num. reflection Rwork: 3666 / Total num. of bins used: 20

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