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- PDB-1a8f: HUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE -

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Basic information

Entry
Database: PDB / ID: 1a8f
TitleHUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE
ComponentsSERUM TRANSFERRIN
KeywordsIRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / NLOBE / IRON-RELEASE / CARBONATE
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / regulation of iron ion transport / HFE-transferrin receptor complex / ferrous iron binding / regulation of protein stability / recycling endosome / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / antibacterial humoral response / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / iron ion transport / cytoplasmic vesicle / secretory granule lumen / vesicle / blood microparticle / transmembrane transporter binding / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin ...Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMacgillivray, R.T.A. / Moore, S.A. / Chen, J. / Anderson, B.F. / Baker, H. / Luo, Y. / Bewley, M. / Smith, C.A. / Murphy, M.E.P. / Wang, Y. ...Macgillivray, R.T.A. / Moore, S.A. / Chen, J. / Anderson, B.F. / Baker, H. / Luo, Y. / Bewley, M. / Smith, C.A. / Murphy, M.E.P. / Wang, Y. / Mason, A.B. / Woodworth, R.C. / Brayer, G.D. / Baker, E.N.
CitationJournal: Biochemistry / Year: 1998
Title: Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release.
Authors: MacGillivray, R.T. / Moore, S.A. / Chen, J. / Anderson, B.F. / Baker, H. / Luo, Y. / Bewley, M. / Smith, C.A. / Murphy, M.E. / Wang, Y. / Mason, A.B. / Woodworth, R.C. / Brayer, G.D. / Baker, E.N.
History
DepositionMar 25, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERUM TRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5243
Polymers36,4081
Non-polymers1162
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.674, 72.674, 154.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SERUM TRANSFERRIN


Mass: 36408.414 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BABY HAMSTER KIDNEY CELLS / Organ: KIDNEY / Production host: Cricetinae (hamsters) / References: UniProt: P02787
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.1
Details: PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM POTASSIUM CACODYLATE, PH 6.1. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM POTASSIUM CACODYLATE, PH ...Details: PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM POTASSIUM CACODYLATE, PH 6.1. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM POTASSIUM CACODYLATE, PH 5.8 - 6.3. PRIOR TO CRYSTALLIZATION, THE PROTEIN WAS DIALYSED AGAINST SODIUM BICARBONATE, PH 8.1, vapor diffusion - sitting drop
PH range: 5.8-6.3
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMpotassium cacodylate1drop
240 %(v/v)ethanol1drop
340 %(v/v)ethanol1reservoir
450 mMpotassium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 36895 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
TNT5Erefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN TRANSFERRIN

Resolution: 1.8→30 Å / Isotropic thermal model: BCORREL (MODIFIED) / Cross valid method: R-FREE / σ(F): 0 / Stereochemistry target values: PROTGEO_EH (MODIFIED)
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1797 5 %RANDOM SELECTION
Rwork0.197 ---
all0.202 36834 --
obs0.202 36834 93.8 %-
Solvent computationSolvent model: BABINET / Bsol: 160 Å2 / ksol: 0.75 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 9 268 2847
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01126472.2
X-RAY DIFFRACTIONt_angle_deg1.535602.5
X-RAY DIFFRACTIONt_dihedral_angle_d19.65850
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009675
X-RAY DIFFRACTIONt_gen_planes0.01338318
X-RAY DIFFRACTIONt_it2.8326315
X-RAY DIFFRACTIONt_nbd0.11392910
Software
*PLUS
Name: TNT / Version: 5EA / Classification: refinement
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.013 / Weight: 18

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