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- PDB-6gje: Structure of the Amnionless(20-357)-Cubilin(36-135) complex -

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Basic information

Entry
Database: PDB / ID: 6gje
TitleStructure of the Amnionless(20-357)-Cubilin(36-135) complex
Components
  • Cubilin
  • Protein amnionless
KeywordsPROTEIN TRANSPORT / receptor / vitamin B12 / cubilin / amnionless / AMN / CUBN / kidney / reabsorption / proximal tubule
Function / homology
Function and homology information


Defective AMN causes MGA1 / Defective CUBN causes MGA1 / Cobalamin (Cbl, vitamin B12) transport and metabolism / excretion / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / HDL clearance / extrinsic component of external side of plasma membrane / cobalamin transport / multicellular organism development ...Defective AMN causes MGA1 / Defective CUBN causes MGA1 / Cobalamin (Cbl, vitamin B12) transport and metabolism / excretion / cobalamin metabolic process / Uptake of dietary cobalamins into enterocytes / HDL clearance / extrinsic component of external side of plasma membrane / cobalamin transport / multicellular organism development / Vitamin D (calciferol) metabolism / tissue homeostasis / high-density lipoprotein particle clearance / Golgi to plasma membrane protein transport / cobalamin binding / cargo receptor activity / lipoprotein transport / microvillus membrane / endocytic vesicle / clathrin-coated pit / cholesterol metabolic process / lysosomal lumen / receptor-mediated endocytosis / establishment of localization in cell / brush border membrane / response to bacterium / protein localization / signaling receptor activity / membrane => GO:0016020 / receptor complex / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / signaling receptor binding / calcium ion binding / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Amnionless / Amnionless / EGF domain / EGF domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Calcium-binding EGF domain ...Amnionless / Amnionless / EGF domain / EGF domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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
Similarity search - Domain/homology
Cubilin / Protein amnionless
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLarsen, C. / Etzerodt, A. / Madsen, M. / Skjoedt, K. / Moestrup, S.K. / Andersen, C.B.F.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research Denmark
CitationJournal: Nat Commun / Year: 2018
Title: Structural assembly of the megadalton-sized receptor for intestinal vitamin B12uptake and kidney protein reabsorption.
Authors: Larsen, C. / Etzerodt, A. / Madsen, M. / Skjodt, K. / Moestrup, S.K. / Andersen, C.B.F.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Feb 27, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 3.0Jun 12, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein amnionless
B: Cubilin
C: Cubilin
D: Cubilin


Theoretical massNumber of molelcules
Total (without water)73,3244
Polymers73,3244
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-82 kcal/mol
Surface area29200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.280, 158.840, 237.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-3706-

HOH

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Components

#1: Protein Protein amnionless


Mass: 35796.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMN, UNQ513/PRO1028 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): ShuffleT7 / References: UniProt: Q9BXJ7
#2: Protein Cubilin / 460 kDa receptor / Intestinal intrinsic factor receptor / Intrinsic factor-cobalamin receptor / ...460 kDa receptor / Intestinal intrinsic factor receptor / Intrinsic factor-cobalamin receptor / Intrinsic factor-vitamin B12 receptor


Mass: 12509.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUBN, IFCR / Plasmid: pACYCDuet-1 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): ShuffleT7 / References: UniProt: O60494
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.51 Å3/Da / Density % sol: 72.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.5 M magnesium sulphate 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 59436 / % possible obs: 100 % / Redundancy: 13.31 % / Net I/σ(I): 19.53
Reflection shellResolution: 2.3→2.4 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.511 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 2562 4.31 %Random selection
Rwork0.2111 ---
obs0.2119 59436 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4445 0 0 98 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044536
X-RAY DIFFRACTIONf_angle_d0.7266143
X-RAY DIFFRACTIONf_dihedral_angle_d18.8971706
X-RAY DIFFRACTIONf_chiral_restr0.071684
X-RAY DIFFRACTIONf_plane_restr0.006823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2967-2.34090.3511330.3042947X-RAY DIFFRACTION94
2.3409-2.38870.31721390.29343089X-RAY DIFFRACTION100
2.3887-2.44060.31421420.28443158X-RAY DIFFRACTION100
2.4406-2.49740.31261410.28713144X-RAY DIFFRACTION100
2.4974-2.55980.29511410.28163119X-RAY DIFFRACTION100
2.5598-2.62910.31031410.28963139X-RAY DIFFRACTION100
2.6291-2.70640.29671420.27453144X-RAY DIFFRACTION100
2.7064-2.79380.24261410.25043145X-RAY DIFFRACTION100
2.7938-2.89360.24251420.24923147X-RAY DIFFRACTION100
2.8936-3.00940.28761420.24533160X-RAY DIFFRACTION100
3.0094-3.14640.25971420.24423145X-RAY DIFFRACTION100
3.1464-3.31220.25821420.23223167X-RAY DIFFRACTION100
3.3122-3.51970.21631440.2053180X-RAY DIFFRACTION100
3.5197-3.79130.2121420.19433176X-RAY DIFFRACTION100
3.7913-4.17270.18241440.18043191X-RAY DIFFRACTION100
4.1727-4.7760.17381460.15813200X-RAY DIFFRACTION100
4.776-6.01530.24991450.19563244X-RAY DIFFRACTION100
6.0153-47.5210.22441530.20923379X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89760.92470.61810.30440.45390.28410.01330.3592-0.28540.15340.11210.08350.16990.3235-00.5735-0.0179-0.01570.5935-0.12930.518551.4143-19.648481.5409
2-0.66390.04191.18751.1430.41011.13090.07010.44010.00060.2107-0.00230.3687-0.1490.07890.39850.2908-0.06350.05080.393-0.15670.330238.027-19.780472.8107
30.97180.70830.94692.48281.01851.415-0.00790.21160.03-0.33330.02160.2608-0.33570.1136-0.01120.37110.0218-0.01380.56-0.14270.550228.5635-26.008459.8895
41.40960.47-0.44120.4921-0.11950.7110.18640.3374-0.3743-0.13480.00610.360.17190.08960.08160.43780.0371-0.14030.6693-0.24880.760221.8223-39.280954.1438
50.0782-0.03220.06720.01280.06770.146-0.12770.4426-0.1936-0.0813-0.17410.6265-0.6155-0.4901-0.02050.6149-0.00730.11180.6399-0.08720.551746.3416-9.390288.2888
60.1039-0.1651-0.14390.49910.80610.31430.09330.10580.07580.1714-0.14760.0712-0.0392-0.082400.5411-0.05750.02160.5217-0.04550.489448.8174-6.594194.9698
73.33910.8076-0.0130.574-0.59090.6571-0.28830.32510.28721.10260.5058-0.6089-0.43630.34750.19510.73760.0502-0.10830.459-0.15480.527363.8307-5.9172103.3951
80.4985-0.01860.39920.0146-0.0040.14940.0213-0.0709-0.06510.43350.040.09650.50530.080800.71180.00880.02520.3815-0.02050.401259.3368.0847116.4534
9-0.09850.00180.05920.02720.00750.0574-0.59050.15960.1138-0.252-0.06070.2754-0.39350.1201.30340.1516-0.00010.7916-0.02920.91657.21434.3992126.9012
10-0.0027-0.0180.00290.0067-0.0001-0.01150.21070.1530.27370.0665-0.06990.42450.01950.871-02.1024-0.37690.42051.1278-0.41141.441564.983148.9834127.112
110.33910.63270.44460.4743-0.04781.3798-0.00660.07720.16860.33730.1414-0.05010.16390.097500.620.0179-0.03790.4746-0.08760.481157.7531-12.682998.4645
120.35490.4668-0.32770.0477-0.08390.2813-0.32650.18940.1668-0.30560.13580.2419-0.66670.12-0.00060.6498-0.0021-0.03080.4474-0.04920.482360.588511.9118106.5503
13-0.0805-0.02440.3651-0.00570.03870.1812-0.55960.2010.51650.5867-0.58880.18090.2840.2248-0.0221.41830.0428-0.32640.5963-0.18770.787465.519836.7999136.0598
140.22010.10230.18190.29140.16040.0372-0.03790.23010.0314-0.01460.1313-0.41640.29650.196200.4723-0.0225-0.04930.6739-0.13050.575163.8924-9.92888.2437
150.0183-0.0648-0.0222-0.0569-0.0222-0.0118-0.3520.4538-0.1990.0621-0.2416-0.0816-0.6265-0.1317-00.576-0.1009-0.06950.6516-0.04310.464455.839-0.234189.1989
160.0921-0.0524-0.13590.06940.05370.2580.12960.3323-0.57871.12460.20840.6852-0.6863-0.08820.01110.7539-0.00690.0540.4152-0.01780.597447.1268-4.339105.15
170.3475-0.23730.10190.08080.08040.07060.0770.01750.1227-0.2563-0.24190.1188-0.2633-0.6011-00.6727-0.0024-0.05520.52440.00580.634352.918813.3953111.1394
180.0704-0.09990.10740.1831-0.20550.1949-0.2259-0.33410.5647-0.0661-0.46940.3708-1.092-0.2798-0.1521.25440.0418-0.25390.5122-0.25620.865763.319729.0441118.9358
190.0519-0.042-0.00020.02310.0256-0.0623-0.5876-0.4836-0.5888-0.2448-0.28620.4796-0.19510.9969-0.00011.7852-0.33020.23171.29810.24791.291871.709537.9992127.121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 276 )
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 357 )
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 63 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 76 )
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 98 )
9X-RAY DIFFRACTION9chain 'B' and (resid 99 through 111 )
10X-RAY DIFFRACTION10chain 'B' and (resid 112 through 120 )
11X-RAY DIFFRACTION11chain 'C' and (resid 37 through 68 )
12X-RAY DIFFRACTION12chain 'C' and (resid 69 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 101 through 119 )
14X-RAY DIFFRACTION14chain 'D' and (resid 37 through 53 )
15X-RAY DIFFRACTION15chain 'D' and (resid 54 through 63 )
16X-RAY DIFFRACTION16chain 'D' and (resid 64 through 76 )
17X-RAY DIFFRACTION17chain 'D' and (resid 77 through 96 )
18X-RAY DIFFRACTION18chain 'D' and (resid 97 through 104 )
19X-RAY DIFFRACTION19chain 'D' and (resid 105 through 118 )

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