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- PDB-1a8e: HUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE -

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Basic information

Entry
Database: PDB / ID: 1a8e
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: 1.6 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 24, 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 / _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 1.4Nov 20, 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
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.120, 57.910, 135.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Cellular location: EXTRACELLULAR / 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.: 138 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: PROTEIN WAS CRYSTALLIZED FROM 26% PEG 4000. BUFFER WAS 40MM NA CACODYLATE, PH 5.75, WITH 20MM NA BICARBONATE. CRYSTALS GROWN AT 4 DEGREES C USING THE HANGING DROP METHOD., vapor diffusion - ...Details: PROTEIN WAS CRYSTALLIZED FROM 26% PEG 4000. BUFFER WAS 40MM NA CACODYLATE, PH 5.75, WITH 20MM NA BICARBONATE. CRYSTALS GROWN AT 4 DEGREES C USING THE HANGING DROP METHOD., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mMsodium cacodylate1reservoir
220 mMsodium bicarbonate1reservoir
326 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1990
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 39418 / % possible obs: 82.4 % / Observed criterion σ(I): 3 / Redundancy: 1.8 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
R-AXISSOFTWAREdata collection
R-AXISSOFTWAREdata reduction
TNT5Erefinement
R-AXISdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RABBIT TRANSFERRIN

Resolution: 1.6→30 Å / Isotropic thermal model: BCORREL (MODIFIED) / σ(F): 0 / Stereochemistry target values: PROTGEO_EH (MODIFIED)
RfactorNum. reflection% reflection
Rwork0.181 --
all-38344 -
obs-38344 80.1 %
Solvent computationSolvent model: BABINET / Bsol: 160 Å2 / ksol: 0.86 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 9 138 2714
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01426450.45
X-RAY DIFFRACTIONt_angle_deg1.3535580.6
X-RAY DIFFRACTIONt_dihedral_angle_d20.75840
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013660.7
X-RAY DIFFRACTIONt_gen_planes0.0163832.6
X-RAY DIFFRACTIONt_it1.8926034
X-RAY DIFFRACTIONt_nbd0.1185291.8
Software
*PLUS
Name: TNT / Version: 5EA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.70
X-RAY DIFFRACTIONt_plane_restr0.0162.6

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