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- PDB-2pmv: Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at... -

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Basic information

Entry
Database: PDB / ID: 2pmv
TitleCrystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution
ComponentsGastric intrinsic factor
KeywordsTRANSPORT PROTEIN / Cobalamin transport protein Alpha6-Alpha6 motif two domain protein
Function / homology
Function and homology information


Defective CBLIF causes IFD / Defective AMN causes MGA1 / Defective CUBN causes MGA1 / cargo receptor ligand activity / Uptake of dietary cobalamins into enterocytes / cobalt ion transport / cobalamin transport / cobalamin binding / microvillus / lysosomal lumen ...Defective CBLIF causes IFD / Defective AMN causes MGA1 / Defective CUBN causes MGA1 / cargo receptor ligand activity / Uptake of dietary cobalamins into enterocytes / cobalt ion transport / cobalamin transport / cobalamin binding / microvillus / lysosomal lumen / endosome / apical plasma membrane / extracellular space / extracellular region
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. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Beta Complex ...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. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COBALAMIN / Cobalamin binding intrinsic factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMathews, F.S. / Gordon, M.M. / Chen, Z. / Rajashankar, K.R. / Ealick, S.E. / Alpers, D.H. / Sukumar, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-A resolution
Authors: Mathews, F.S. / Gordon, M.M. / Chen, Z. / Rajashankar, K.R. / Ealick, S.E. / Alpers, D.H. / Sukumar, N.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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.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 / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: Gastric intrinsic factor
B: Gastric intrinsic factor
C: Gastric intrinsic factor
D: Gastric intrinsic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,3038
Polymers173,7944
Non-polymers3,5104
Water8,269459
1
A: Gastric intrinsic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2033
Polymers43,4481
Non-polymers1,7552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gastric intrinsic factor


Theoretical massNumber of molelcules
Total (without water)43,4481
Polymers43,4481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Gastric intrinsic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2033
Polymers43,4481
Non-polymers1,7552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Gastric intrinsic factor


Theoretical massNumber of molelcules
Total (without water)43,4481
Polymers43,4481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.100, 67.300, 147.700
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

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


Mass: 43448.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P27352
#2: 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.: 2
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
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG20000, 100mM MES, 20mM CaCL2 and 9mM BaCL2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 1.6059 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6059 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 61149 / Num. obs: 55707 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / % possible all: 54.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→37.53 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 491016.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1529 3 %RANDOM
Rwork0.213 ---
obs0.213 50885 93.4 %-
all-54502 --
Displacement parametersBiso mean: 56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9760 0 238 459 10457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 238 3.2 %
Rwork0.31 7090 -
obs--81.8 %

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