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- PDB-3kq4: Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin -

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Basic information

Entry
Database: PDB / ID: 3kq4
TitleStructure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin
Components
  • Cubilin
  • Gastric intrinsic factor
KeywordsTRANSPORT PROTEIN / PROTEIN-PROTEIN COMPLEX / Cobalt / Cobalt transport / Disease mutation / Disulfide bond / Glycoprotein / Secreted / Transport / Cholesterol metabolism / Cobalamin / EGF-like domain / Endocytosis / Endosome / Lipid metabolism / Lysosome / Membrane / Protein transport / Receptor / Steroid metabolism
Function / homology
Function and homology information


Defective CBLIF causes IFD / Defective AMN causes MGA1 / Defective CUBN causes MGA1 / cargo receptor ligand activity / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / HDL clearance / cobalt ion transport / extrinsic component of external side of plasma membrane / cobalamin transport ...Defective CBLIF causes IFD / Defective AMN causes MGA1 / Defective CUBN causes MGA1 / cargo receptor ligand activity / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / HDL clearance / cobalt ion transport / extrinsic component of external side of plasma membrane / cobalamin transport / Vitamin D (calciferol) metabolism / tissue homeostasis / cobalamin binding / cargo receptor activity / lipoprotein transport / microvillus membrane / microvillus / endocytic vesicle / clathrin-coated pit / cholesterol metabolic process / receptor-mediated endocytosis / lysosomal lumen / establishment of localization in cell / brush border membrane / response to bacterium / signaling receptor activity / receptor complex / endosome / apical plasma membrane / lysosomal membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Spermadhesin, CUB domain / EGF domain / EGF domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / CUB domain ...Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Spermadhesin, CUB domain / EGF domain / EGF domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Glycosyltransferase - #20 / Calcium-binding EGF domain / Glycosyltransferase / Alpha/alpha barrel / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COBALAMIN / Cubilin / Cobalamin binding intrinsic factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAndersen, C.B.F. / Madsen, M. / Moestrup, S.K. / Andersen, G.R.
CitationJournal: Nature / Year: 2010
Title: Structural basis for receptor recognition of vitamin-B(12)-intrinsic factor complexes.
Authors: Andersen, C.B. / Madsen, M. / Storm, T. / Moestrup, S.K. / Andersen, G.R.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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_conn_angle / struct_asym / struct_conn / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
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: Gastric intrinsic factor
B: Cubilin
C: Gastric intrinsic factor
D: Cubilin
E: Gastric intrinsic factor
F: Cubilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,19051
Polymers283,3356
Non-polymers15,85645
Water0
1
A: Gastric intrinsic factor
B: Cubilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,73017
Polymers94,4452
Non-polymers5,28515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint8 kcal/mol
Surface area39900 Å2
MethodPISA
2
C: Gastric intrinsic factor
D: Cubilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,73017
Polymers94,4452
Non-polymers5,28515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint8 kcal/mol
Surface area39890 Å2
MethodPISA
3
E: Gastric intrinsic factor
F: Cubilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,73017
Polymers94,4452
Non-polymers5,28515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint8 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.684, 204.179, 410.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 932:1388 )
211chain D and (resseq 932:1388 )
311chain F and (resseq 932:1388 )
112chain A and (resseq 7:281 or resseq 290:399 )
212chain C and (resseq 7:281 or resseq 290:399 )
312chain E and (resseq 7:281 or resseq 290:399 )

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Gastric intrinsic factor / Intrinsic factor / INF / IF


Mass: 42815.770 Da / Num. of mol.: 3 / Fragment: UNP residues 25-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GIF, IFMH / Production host: Pichia Pastoris (fungus) / References: UniProt: P27352
#2: Protein Cubilin / / Intrinsic factor-cobalamin receptor / Intrinsic factor-vitamin B12 receptor / 460 kDa receptor / ...Intrinsic factor-cobalamin receptor / Intrinsic factor-vitamin B12 receptor / 460 kDa receptor / Intestinal intrinsic factor receptor


Mass: 51629.082 Da / Num. of mol.: 3 / Fragment: UNP residues 932-1388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUBN, IFCR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O60494

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Sugars , 3 types, 30 molecules

#3: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 15 molecules

#6: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca

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Details

Sequence detailsGLN TO HIS SEQUENCE CONFLICT IN UNP ENTRY P27352

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.35 Å3/Da / Density % sol: 71.7 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.9
SYNCHROTRONMAX II I911-321.8
Detector
IDDate
1Feb 20, 2009
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.81
ReflectionResolution: 3.3→50 Å / Num. all: 74572 / Num. obs: 72280 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→47.848 Å / SU ML: 0.38 / σ(F): 2.01 / Phase error: 23.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 1102 1.52 %
Rwork0.2109 --
obs0.2114 72265 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.419 Å2 / ksol: 0.297 e/Å3
Refinement stepCycle: LAST / Resolution: 3.3→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19764 0 1029 0 20793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321450
X-RAY DIFFRACTIONf_angle_d1.9329349
X-RAY DIFFRACTIONf_dihedral_angle_d26.39812915
X-RAY DIFFRACTIONf_chiral_restr0.1383324
X-RAY DIFFRACTIONf_plane_restr0.0073660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3640X-RAY DIFFRACTIONPOSITIONAL
12D3640X-RAY DIFFRACTIONPOSITIONAL0.006
13F3640X-RAY DIFFRACTIONPOSITIONAL0.005
21A2737X-RAY DIFFRACTIONPOSITIONAL
22C2737X-RAY DIFFRACTIONPOSITIONAL0.004
23E2737X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.45010.35651700.28738921X-RAY DIFFRACTION98
3.4501-3.6320.30781780.26178797X-RAY DIFFRACTION98
3.632-3.85940.2682700.23179008X-RAY DIFFRACTION98
3.8594-4.15730.21321070.1988977X-RAY DIFFRACTION98
4.1573-4.57530.1834950.17328902X-RAY DIFFRACTION97
4.5753-5.23670.21811290.17368866X-RAY DIFFRACTION97
5.2367-6.5950.2371750.19878826X-RAY DIFFRACTION96
6.595-47.85280.22321780.21058866X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -55.3989 Å / Origin y: 15.1433 Å / Origin z: -49.3363 Å
111213212223313233
T0.4521 Å2-0.0535 Å2-0.0508 Å2-0.3465 Å2-0.0028 Å2--0.4564 Å2
L0.0141 °2-0.0965 °20.0719 °2-0.1055 °2-0.1007 °2--0.4342 °2
S0.0062 Å °-0.0196 Å °-0.01 Å °-0.0661 Å °-0.0344 Å °0.0069 Å °-0.0361 Å °-0.0347 Å °0.0254 Å °
Refinement TLS groupSelection details: all

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