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- PDB-2hau: Apo-Human Serum Transferrin (Non-Glycosylated) -

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Basic information

Entry
Database: PDB / ID: 2hau
TitleApo-Human Serum Transferrin (Non-Glycosylated)
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Serotransferrin / human / iron transporter / apo / iron-free
Function / homology
Function and homology information


iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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-like domain / Transferrin / 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-like domain / Transferrin / 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
CITRIC ACID / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsWally, J. / Everse, S.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Crystal Structure of Iron-free Human Serum Transferrin Provides Insight into Inter-lobe Communication and Receptor Binding.
Authors: Wally, J. / Halbrooks, P.J. / Vonrhein, C. / Rould, M.A. / Everse, S.J. / Mason, A.B. / Buchanan, S.K.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serotransferrin
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7478
Polymers150,7942
Non-polymers9536
Water00
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6813
Polymers75,3971
Non-polymers2842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0665
Polymers75,3971
Non-polymers6684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.996, 102.159, 197.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Serotransferrin / Transferrin / Siderophilin / Beta-1-metal-binding globulin


Mass: 75397.164 Da / Num. of mol.: 2 / Mutation: N413D,N611D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Cell (production host): Kidney cell / Organ (production host): Kidney / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 15 mg/ml protein, 0.3 M ammonium citrate, 16-18% PEG 3350 , pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
31031
41031
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.935
SYNCHROTRONNSLS X2520.9794
SYNCHROTRONNSLS X26C30.9641, 0.9790, 1.100
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 27, 2006
ADSC QUANTUM 3152CCDMar 23, 2002
ADSC QUANTUM 43CCDApr 27, 2006
ADSC QUANTUM 44CCDApr 28, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2MADMx-ray1
3MADMx-ray1
4MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9351
20.97941
30.96411
40.9791
51.11
ReflectionResolution: 2.7→50 Å / Num. obs: 47968 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.2 / % possible all: 83.6

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Processing

Software
NameClassification
DENZOdata reduction
SHARPphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.324 2343 RANDOM
Rwork0.273 --
all0.273 47503 -
obs0.273 45160 -
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10488 0 64 0 10552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.33

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