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- PDB-6p8i: N-terminal 5 domains of IGFIIR -

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Basic information

Entry
Database: PDB / ID: 6p8i
TitleN-terminal 5 domains of IGFIIR
ComponentsCation-independent mannose-6-phosphate receptor
KeywordsSUGAR BINDING PROTEIN / Lectin / receptor / mannose-6-phosphate / protein transport
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsOlson, L.J. / Dahms, N.M. / Kim, J.-J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1DK042667 United States
CitationJournal: Commun Biol / Year: 2020
Title: Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor.
Authors: Olson, L.J. / Misra, S.K. / Ishihara, M. / Battaile, K.P. / Grant, O.C. / Sood, A. / Woods, R.J. / Kim, J.P. / Tiemeyer, M. / Ren, G. / Sharp, J.S. / Dahms, N.M.
History
DepositionJun 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_close_contact / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 30, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2462
Polymers81,4971
Non-polymers7491
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.788, 66.228, 123.070
Angle α, β, γ (deg.)90.000, 99.180, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Cation-independent mannose-6-phosphate receptor / M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / ...M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / Insulin-like growth factor II receptor / IGF-II receptor / M6P/IGF2 receptor / M6P/IGF2R


Mass: 81497.133 Da / Num. of mol.: 1 / Fragment: N-terminal 5 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11717
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100mM ammonium citrate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.54→40 Å / Num. obs: 48916 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 55.72 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.875 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.55-2.592.90.64912701.341198
2.59-2.6430.57212951.399198.4
2.64-2.6930.60513092.924199.1
2.69-2.7530.43712821.48199.1
2.75-2.813.10.37713311.51199
2.81-2.873.10.32313201.552199.5
2.87-2.943.10.28112861.537199.2
2.94-3.023.20.21913331.602199.5
3.02-3.113.30.17713091.651199.5
3.11-3.213.30.14413121.7199.3
3.21-3.333.30.11813301.842199.6
3.33-3.463.40.11613072.915199.5
3.46-3.623.40.08113271.395199.3
3.62-3.813.40.08813231.7241100
3.81-4.053.40.08813082.302199.7
4.05-4.363.40.04413362.133199.7
4.36-4.83.40.03413282.007199.7
4.8-5.493.40.03213411.93199.7
5.49-6.913.40.03513452.094199.7
6.91-403.30.02613852.194198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.54 Å39.97 Å
Translation2.54 Å39.97 Å

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q25,

1q25


Resolution: 2.54→39.97 Å / SU ML: 0.4122 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3203
RfactorNum. reflection% reflection
Rfree0.2822 3646 7.45 %
Rwork0.2242 --
obs0.2285 48915 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.86 Å2
Refinement stepCycle: LAST / Resolution: 2.54→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 50 28 5295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785377
X-RAY DIFFRACTIONf_angle_d1.10577278
X-RAY DIFFRACTIONf_chiral_restr0.0599811
X-RAY DIFFRACTIONf_plane_restr0.0053936
X-RAY DIFFRACTIONf_dihedral_angle_d9.2683752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.580.3895880.31421344X-RAY DIFFRACTION73.32
2.58-2.610.34661470.31041666X-RAY DIFFRACTION91.29
2.61-2.650.3641320.30661708X-RAY DIFFRACTION90.37
2.65-2.690.34491410.31961686X-RAY DIFFRACTION92.09
2.69-2.730.32431400.31715X-RAY DIFFRACTION92.75
2.73-2.780.35941460.29081734X-RAY DIFFRACTION92.84
2.78-2.820.38341160.29861781X-RAY DIFFRACTION94
2.82-2.880.36651650.28181727X-RAY DIFFRACTION94.88
2.88-2.930.28811350.28121695X-RAY DIFFRACTION94.09
2.93-2.990.29211510.25651770X-RAY DIFFRACTION94.17
2.99-3.060.30871340.2561731X-RAY DIFFRACTION94.62
3.06-3.130.3311390.25991756X-RAY DIFFRACTION95.71
3.13-3.20.31451590.24741783X-RAY DIFFRACTION94.69
3.2-3.290.29991400.25631754X-RAY DIFFRACTION95.8
3.29-3.390.31911420.24471792X-RAY DIFFRACTION96.27
3.39-3.50.32991390.22981766X-RAY DIFFRACTION95.63
3.5-3.620.32451440.23481787X-RAY DIFFRACTION95.83
3.62-3.770.29191380.22681744X-RAY DIFFRACTION95.82
3.77-3.940.26021530.21681816X-RAY DIFFRACTION96.47
3.94-4.150.28271560.20231734X-RAY DIFFRACTION95.99
4.15-4.410.23811370.18851795X-RAY DIFFRACTION96.79
4.41-4.750.22931370.17471791X-RAY DIFFRACTION96.3
4.75-5.220.22741470.16571797X-RAY DIFFRACTION96.91
5.22-5.970.23391510.19951786X-RAY DIFFRACTION96.75
5.98-7.520.31071380.22681808X-RAY DIFFRACTION97.35
7.53-39.970.23291310.21481803X-RAY DIFFRACTION96.94

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