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- PDB-3v89: The crystal structure of transferrin binding protein A (TbpA) fro... -

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Basic information

Entry
Database: PDB / ID: 3v89
TitleThe crystal structure of transferrin binding protein A (TbpA) from Neisseria meningitidis serogroup B in complex with the C-lobe of human transferrin
Components
  • Serotransferrin
  • Transferrin-binding protein A
KeywordsMEMBRANE PROTEIN/METAL TRANSPORT / tonB-dependent transporter / iron binding / MEMBRANE PROTEIN-METAL TRANSPORT complex
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / 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 ...ferric iron transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / 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 / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / osteoclast differentiation / ferric iron binding / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / cell outer membrane / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of iron ion transport / regulation of protein stability / HFE-transferrin receptor complex / 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) / late endosome / Cargo recognition for clathrin-mediated endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / antibacterial humoral response / Clathrin-mediated endocytosis / iron ion transport / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / 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
TonB-dependent lactoferrin/transferrin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / Serotransferrin, mammalian / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site ...TonB-dependent lactoferrin/transferrin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / Serotransferrin, mammalian / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / 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 / Beta Complex / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serotransferrin / Transferrin-binding protein A / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNoinaj, N. / Oke, M. / Easley, N. / Zak, O. / Aisen, P. / Buchanan, S.K.
CitationJournal: Nature / Year: 2012
Title: Structural basis for iron piracy by pathogenic Neisseria.
Authors: Noinaj, N. / Easley, N.C. / Oke, M. / Mizuno, N. / Gumbart, J. / Boura, E. / Steere, A.N. / Zak, O. / Aisen, P. / Tajkhorshid, E. / Evans, R.W. / Gorringe, A.R. / Mason, A.B. / Steven, A.C. / Buchanan, S.K.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transferrin-binding protein A
B: Serotransferrin


Theoretical massNumber of molelcules
Total (without water)139,3842
Polymers139,3842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-9 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.054, 107.592, 130.719
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transferrin-binding protein A


Mass: 101181.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: tbpA / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JPJ0, UniProt: Q9K0U9*PLUS
#2: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 38202.324 Da / Num. of mol.: 1 / Fragment: C-lobe (UNP residues 356-698)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / References: UniProt: P02787
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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG 1000, 100mM sodium acetate buffer (pH 4.8), 200mM NaCl, 0.1% LDAO and 3% heptane-1,2,3-triol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 18, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 28265 / Num. obs: 28265 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 20.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.24 / % possible all: 76.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_865)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.959 Å / SU ML: 1 / σ(F): 1.34 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1401 4.96 %random
Rwork0.2242 ---
obs0.2273 28265 96.81 %-
all-28265 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.322 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.5225 Å2-0 Å2-9.9722 Å2
2---11.8189 Å20 Å2
3---4.2963 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9110 0 0 0 9110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059329
X-RAY DIFFRACTIONf_angle_d1.12512629
X-RAY DIFFRACTIONf_dihedral_angle_d17.643308
X-RAY DIFFRACTIONf_chiral_restr0.0911348
X-RAY DIFFRACTIONf_plane_restr0.0041670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.21070.4361300.32062239X-RAY DIFFRACTION82
3.2107-3.33910.36181140.28272528X-RAY DIFFRACTION92
3.3391-3.49090.3071410.25842681X-RAY DIFFRACTION96
3.4909-3.67460.30161520.24382755X-RAY DIFFRACTION100
3.6746-3.90440.32721450.23932750X-RAY DIFFRACTION100
3.9044-4.20510.31400.21722763X-RAY DIFFRACTION100
4.2051-4.62690.2361530.18742742X-RAY DIFFRACTION100
4.6269-5.29320.24681400.18472801X-RAY DIFFRACTION100
5.2932-6.65680.27581420.22062779X-RAY DIFFRACTION100
6.6568-29.96040.26231440.21612826X-RAY DIFFRACTION99
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29540.43290.67980.2918-0.09571.429-0.0383-0.63180.33850.93430.0524-0.4118-0.17280.0204-0.01510.94020.1088-0.25680.5432-0.1450.5856-7.5110.3626-19.8046
20.86740.47531.06562.57261.53153.6638-0.16-0.3350.26490.0145-0.24040.3604-0.6694-0.5360.44470.28350.11820.0310.3429-0.09070.5194-24.2646-9.9191-42.6326
31.55880.68221.18142.32751.55732.6658-0.048-0.62630.25870.9308-0.0915-0.02280.1884-0.33880.12790.73530.04340.020.4858-0.06080.3691-18.2023-14.3804-26.951
41.59950.6331.81623.76624.43347.28080.115-0.1479-0.20230.5107-0.59390.71260.4502-0.80690.42670.2785-0.08630.11620.30950.00970.5356-33.8563-38.6629-56.8902
50.3941-0.3822-0.00370.29340.11440.01230.2584-0.315-0.1781.31240.1686-0.87730.55010.0137-0.41481.42970.0841-0.46620.7769-0.03030.70443.3767-13.1691-12.3047
61.44610.38770.82162.95320.13871.84680.0066-0.10160.09520.43040.1104-0.5461-0.05910.3411-0.08370.59450.0231-0.22210.5113-0.12170.58763.7756-0.7048-30.5479
73.3453-0.16330.75533.3408-0.40010.56770.32580.2306-0.95040.68390.1451-1.01820.54380.5293-0.45490.80350.1786-0.40430.5619-0.21481.01682.8676-45.05-43.3679
82.85680.6450.80823.14091.24273.47160.12190.1273-0.4079-0.11330.3455-1.28780.29460.4372-0.42860.2187-0.0270.0670.362-0.07530.757-11.5612-49.1865-67.8576
90.25120.59930.48821.16760.95851.60080.6392-0.1859-1.09380.8105-0.0376-0.44051.1288-0.0147-0.55070.75330.0293-0.24620.392-0.04010.7091-6.1942-44.9892-41.7662
100.96311.44513.30179.72036.10842.00290.12931.01990.0624-0.2730.40610.7145-1.2707-0.0016-0.49720.4455-0.0816-0.04250.7996-0.09450.81530.6151-29.1307-46.3783
113.65361.94880.77028.28223.2522.9668-0.23190.1966-0.73760.80750.6672-0.53841.28540.0994-0.54610.76660.0164-0.2720.5670.05160.8647-7.7286-53.7704-47.7738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 52:203)
2X-RAY DIFFRACTION2chain 'A' and (resseq 204:326)
3X-RAY DIFFRACTION3chain 'A' and (resseq 327:515)
4X-RAY DIFFRACTION4chain 'A' and (resseq 516:562)
5X-RAY DIFFRACTION5chain 'A' and (resseq 563:686)
6X-RAY DIFFRACTION6chain 'A' and (resseq 687:915)
7X-RAY DIFFRACTION7chain 'B' and (resseq 337:421)
8X-RAY DIFFRACTION8chain 'B' and (resseq 422:573)
9X-RAY DIFFRACTION9chain 'B' and (resseq 574:608)
10X-RAY DIFFRACTION10chain 'B' and (resseq 609:628)
11X-RAY DIFFRACTION11chain 'B' and (resseq 629:675)

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