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- PDB-3v8x: The crystal structure of transferrin binding protein A (TbpA) fro... -

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Basic information

Entry
Database: PDB / ID: 3v8x
TitleThe crystal structure of transferrin binding protein A (TbpA) from Neisserial meningitidis serogroup B in complex with full length human transferrin
Components
  • Serotransferrin
  • Transferrin-binding protein 1
KeywordsMEMBRANE PROTEIN/METAL TRANSPORT / iron binding protein / transferrin binding protein A / iron binding/scavenging / MEMBRANE PROTEIN-METAL TRANSPORT complex
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / siderophore transmembrane transport / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / siderophore uptake transmembrane transporter activity / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption ...ferric iron transmembrane transporter activity / siderophore transmembrane transport / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / siderophore uptake transmembrane transporter activity / 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 / cell outer membrane / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of protein stability / 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
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 (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / 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
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNoinaj, N. / Easley, N. / 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 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
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_validate_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_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: Transferrin-binding protein 1
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,6836
Polymers178,3672
Non-polymers4,3164
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint66 kcal/mol
Surface area64870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.014, 129.362, 198.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Transferrin-binding protein 1


Mass: 101213.328 Da / Num. of mol.: 1 / Mutation: M913Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: tbp1, NMB0461 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K0U9
#2: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 77153.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / References: UniProt: P02787

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Sugars , 2 types, 2 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1932.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-4DManpa1-3[DGalpb1-4DGlcpNAcb1-4DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-1-4-5-3-1-4/a4-b1_b4-c1_c3-d1_c6-h1_d4-e1_e4-f1_f6-g2_h4-i1_i4-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1770.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-4DManpa1-6[DGlcpNAcb1-4DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-1-3-1-4-5/a4-b1_b4-c1_c3-d1_c6-f1_d4-e1_f4-g1_g4-h1_h6-i2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 206 molecules

#5: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.28 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Peg3350 and 200 mM BaBr2, pH 7.5, 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
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 71620 / Num. obs: 71620 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.12 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.84 / % possible all: 97.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.924 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 3601 5.03 %
Rwork0.2081 --
obs0.2111 71619 98.44 %
all-71620 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.919 Å2 / ksol: 0.286 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5828 Å2-0 Å2-0 Å2
2---3.2356 Å2-0 Å2
3----3.3471 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11714 0 293 204 12211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412341
X-RAY DIFFRACTIONf_angle_d1.3616717
X-RAY DIFFRACTIONf_dihedral_angle_d19.5414510
X-RAY DIFFRACTIONf_chiral_restr0.0611825
X-RAY DIFFRACTIONf_plane_restr0.0032166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63420.39291030.36432334X-RAY DIFFRACTION89
2.6342-2.67030.38711320.35552566X-RAY DIFFRACTION97
2.6703-2.70840.41671460.34552551X-RAY DIFFRACTION99
2.7084-2.74880.39221330.35892613X-RAY DIFFRACTION99
2.7488-2.79170.36971450.31722588X-RAY DIFFRACTION99
2.7917-2.83750.37771280.29892608X-RAY DIFFRACTION99
2.8375-2.88630.31571340.27452600X-RAY DIFFRACTION99
2.8863-2.93880.3681550.28192599X-RAY DIFFRACTION99
2.9388-2.99530.34441470.27382572X-RAY DIFFRACTION99
2.9953-3.05630.32491340.25642608X-RAY DIFFRACTION99
3.0563-3.12270.30911300.24242603X-RAY DIFFRACTION99
3.1227-3.19530.28011120.21792634X-RAY DIFFRACTION99
3.1953-3.27510.25551480.21772605X-RAY DIFFRACTION99
3.2751-3.36350.28451320.21212651X-RAY DIFFRACTION99
3.3635-3.46240.27291570.20382601X-RAY DIFFRACTION99
3.4624-3.5740.25431300.19892648X-RAY DIFFRACTION99
3.574-3.70150.24671470.18812637X-RAY DIFFRACTION99
3.7015-3.84940.22951500.18232620X-RAY DIFFRACTION99
3.8494-4.02420.24291420.17932645X-RAY DIFFRACTION99
4.0242-4.23580.24061310.16072646X-RAY DIFFRACTION99
4.2358-4.50030.18611590.15382640X-RAY DIFFRACTION99
4.5003-4.84650.18551300.1442666X-RAY DIFFRACTION99
4.8465-5.33170.23321400.16812659X-RAY DIFFRACTION99
5.3317-6.09760.25271500.20242669X-RAY DIFFRACTION98
6.0976-7.66090.30531180.18932708X-RAY DIFFRACTION98
7.6609-29.92550.27541680.22412747X-RAY DIFFRACTION97
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)
11.15910.02360.2141.3166-0.32091.38490.0183-0.5204-0.31150.59830.0549-0.14750.11910.0109-0.05070.62570.0131-0.12680.60780.19620.484334.2542-52.365941.3379
21.8511-1.11541.17251.6239-1.05431.6354-0.191-0.5722-0.14070.39330.23450.1485-0.1289-0.4141-0.02020.41420.0221-0.01660.49510.03970.34967.576-35.817824.6932
33.0215-1.34170.79651.9939-0.52341.71250.1176-0.1065-0.41330.0946-0.0439-0.18380.33470.1894-0.06980.39390.0217-0.0510.30960.07670.385234.0756-49.587827.3137
46.4269-2.47771.97722.3362-0.43790.65490.17930.6205-0.1383-0.1947-0.1610.4378-0.12910.0176-0.02020.38550.0816-0.02760.48940.03470.29685.6784-26.7354.4654
52.048-0.60642.47471.9246-0.57022.70010.1333-0.0004-0.04450.3691-0.2585-0.60890.26280.48820.00550.4507-0.0644-0.22520.63530.16240.70254.4004-44.195939.3016
61.12820.06340.15360.83980.44551.2911-0.2014-0.24070.08970.4689-0.0843-0.6068-0.48010.65250.2760.6902-0.0266-0.29460.6286-0.02190.640747.8987-29.974138.2163
71.56350.3526-0.41350.8702-1.70872.1144-0.2698-0.4568-0.09920.55180.2368-0.2326-0.3093-0.14230.06681.11330.0759-0.17690.84070.08230.427537.5097-39.511255.6364
81.62670.6528-0.60344.1196-2.7263.19940.0427-0.71090.06441.3926-0.1888-0.2067-0.7624-0.07240.23760.77950.0743-0.10780.79220.05790.362328.8924-36.411249.8796
91.22090.2419-0.76091.69590.50231.7295-0.2422-0.37190.02231.39020.4238-0.3552-0.5132-0.5379-0.21720.78840.16-0.13440.86570.15370.453421.0436-40.732846.7788
102.2343-0.9309-0.81544.65220.95731.99970.24640.14060.7913-0.2707-0.0136-0.272-0.83080.2346-0.11670.7061-0.137-0.02730.36030.10480.700149.24338.0617-8.2706
113.23460.48190.47280.70420.16510.3792-0.1657-0.02830.6981-0.09120.00460.1671-0.4619-0.14470.13360.76240.08-0.12910.3783-0.02820.55117.0248-3.46389.8064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 54:228)
2X-RAY DIFFRACTION2chain 'A' and (resseq 229:382)
3X-RAY DIFFRACTION3chain 'A' and (resseq 383:513)
4X-RAY DIFFRACTION4chain 'A' and (resseq 514:574)
5X-RAY DIFFRACTION5chain 'A' and (resseq 575:657)
6X-RAY DIFFRACTION6chain 'A' and (resseq 658:728)
7X-RAY DIFFRACTION7chain 'A' and (resseq 729:813)
8X-RAY DIFFRACTION8chain 'A' and (resseq 814:867)
9X-RAY DIFFRACTION9chain 'A' and (resseq 868:915)
10X-RAY DIFFRACTION10chain 'B' and (resseq 4:341)
11X-RAY DIFFRACTION11chain 'B' and (resseq 342:679)

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