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- PDB-4kki: Crystal Structure of Haptocorrin in Complex with CNCbl -

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Basic information

Entry
Database: PDB / ID: 4kki
TitleCrystal Structure of Haptocorrin in Complex with CNCbl
ComponentsTranscobalamin-1
KeywordsTRANSPORT PROTEIN / Cobalamin transport protein / alpha6-alpha6 helical barrel
Function / homology
Function and homology information


Transport of RCbl within the body / cargo receptor ligand activity / Uptake of dietary cobalamins into enterocytes / cobalt ion transport / cobalamin transport / molecular sequestering activity / cobalamin binding / specific granule lumen / tertiary granule lumen / Neutrophil degranulation ...Transport of RCbl within the body / cargo receptor ligand activity / Uptake of dietary cobalamins into enterocytes / cobalt ion transport / cobalamin transport / molecular sequestering activity / cobalamin binding / specific granule lumen / tertiary granule lumen / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Glycosyltransferase ...Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CYANOCOBALAMIN / DI(HYDROXYETHYL)ETHER / Transcobalamin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFurger, E. / Frei, D.C. / Schibli, R. / Fischer, E. / Prota, A.E.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis for universal corrinoid recognition by the cobalamin transport protein haptocorrin.
Authors: Furger, E. / Frei, D.C. / Schibli, R. / Fischer, E. / Prota, A.E.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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 2.0Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,30921
Polymers52,1971
Non-polymers4,11220
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.890, 149.890, 57.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein / Sugars , 2 types, 8 molecules A

#1: Protein Transcobalamin-1 / TC-1 / Transcobalamin I / TC I / TCI


Mass: 52196.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 GnTI- / Gene: TC1, TCN1 / Plasmid: pcDNA4/myc-His A / Production host: Homo Sapiens (human) / References: UniProt: P20061
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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 , 4 types, 147 molecules

#3: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 50% PEG 400, 0.2M magnesium chloride, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0015
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2011
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR, SAGITTALLY - HORIZONTALLY FOCUSSED
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2.35→49 Å / Num. obs: 31018 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.485 / Mean I/σ(I) obs: 1.89 / Rsym value: 1.485 / % possible all: 100

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2PMV, 2BB6

2pmv

2bb6


Resolution: 2.35→49 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1565 5.05 %
Rwork0.196 --
obs0.197 31015 100 %
all-31018 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 269 134 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023444
X-RAY DIFFRACTIONf_angle_d0.6834661
X-RAY DIFFRACTIONf_dihedral_angle_d14.0371303
X-RAY DIFFRACTIONf_chiral_restr0.046534
X-RAY DIFFRACTIONf_plane_restr0.002571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.42580.30221570.26872652X-RAY DIFFRACTION100
2.4258-2.51250.28121350.25262670X-RAY DIFFRACTION100
2.5125-2.61310.29161280.2282651X-RAY DIFFRACTION100
2.6131-2.7320.29221340.22082672X-RAY DIFFRACTION100
2.732-2.8760.2891370.22182660X-RAY DIFFRACTION100
2.876-3.05620.25811360.21762680X-RAY DIFFRACTION100
3.0562-3.29210.2461510.22142622X-RAY DIFFRACTION100
3.2921-3.62330.23861500.19612688X-RAY DIFFRACTION100
3.6233-4.14740.22431220.17522703X-RAY DIFFRACTION100
4.1474-5.22440.19561680.16452684X-RAY DIFFRACTION100
5.2244-49.07370.19371470.19422768X-RAY DIFFRACTION100
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4661-0.2342-0.42332.01360.32491.8127-0.058-0.0157-0.18870.0238-0.02590.0503-0.0191-0.08970.2079-0.015-0.02580.25630.0390.2608-27.55348.97217.5992
21.03850.08010.59850.33110.2290.3384-0.14370.0562-0.04270.0460.0877-0.09330.09430.42520.3184-0.022-0.02330.68710.02680.4658-1.387745.484813.6403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:294)
2X-RAY DIFFRACTION2(chain A and resid 331:411)

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