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- PDB-3aih: Human OS-9 MRH domain complexed with alpha3,alpha6-Man5 -

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Basic information

Entry
Database: PDB / ID: 3aih
TitleHuman OS-9 MRH domain complexed with alpha3,alpha6-Man5
ComponentsProtein OS-9
KeywordsSUGAR BINDING PROTEIN / Beta barrel / Lectin
Function / homology
Function and homology information


endoplasmic reticulum mannose trimming / negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / protein retention in ER lumen / : / endoplasmic reticulum quality control compartment / retrograde protein transport, ER to cytosol / protein targeting / ER Quality Control Compartment (ERQC) / response to endoplasmic reticulum stress ...endoplasmic reticulum mannose trimming / negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / protein retention in ER lumen / : / endoplasmic reticulum quality control compartment / retrograde protein transport, ER to cytosol / protein targeting / ER Quality Control Compartment (ERQC) / response to endoplasmic reticulum stress / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / ABC-family proteins mediated transport / transmembrane transport / ubiquitin-dependent protein catabolic process / carbohydrate binding / protease binding / protein ubiquitination / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Protein OS9-like domain / Glucosidase II beta subunit-like protein / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSatoh, T. / Chen, Y. / Hu, D. / Hanashima, S. / Yamamoto, K. / Yamaguchi, Y.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural Basis for Oligosaccharide Recognition of Misfolded Glycoproteins by OS-9 in ER-Associated Degradation
Authors: Satoh, T. / Chen, Y. / Hu, D. / Hanashima, S. / Yamamoto, K. / Yamaguchi, Y.
History
DepositionMay 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 17, 2014Group: Atomic model / Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein OS-9
B: Protein OS-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8494
Polymers28,8402
Non-polymers1,0092
Water1,42379
1
A: Protein OS-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9252
Polymers14,4201
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein OS-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9252
Polymers14,4201
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.1, 73.1, 180.3
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-24-

HOH

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Components

#1: Protein Protein OS-9 / Amplified in osteosarcoma 9


Mass: 14420.070 Da / Num. of mol.: 2 / Fragment: MRH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OS9 / Plasmid: pCold-I (MBP fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q13438
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE MODELS ARE BASED ON SOLUTION NMR ANALYSES.

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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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.9M ammonium sulfate, 0.1M Tris-HCl, 2% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17542 / Num. obs: 17480 / % possible obs: 99.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 28.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1694 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.571 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 881 5.1 %RANDOM
Rwork0.228 ---
obs0.23 16555 99.89 %-
all-16555 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.263 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.59 Å20 Å2
2---1.19 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 68 79 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211939
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9682626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42722.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23115310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2911517
X-RAY DIFFRACTIONr_chiral_restr0.1230.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211473
X-RAY DIFFRACTIONr_mcbond_it1.1331.51092
X-RAY DIFFRACTIONr_mcangle_it2.10321749
X-RAY DIFFRACTIONr_scbond_it2.7743847
X-RAY DIFFRACTIONr_scangle_it4.4054.5877
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 54 -
Rwork0.267 1205 -
obs--100 %

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