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- PDB-3bsz: Crystal structure of the transthyretin-retinol binding protein-Fa... -

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Basic information

Entry
Database: PDB / ID: 3bsz
TitleCrystal structure of the transthyretin-retinol binding protein-Fab complex
Components
  • (Fab fragment ...) x 2
  • Plasma retinol-binding protein
  • Transthyretin
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / retinol / Vitamin A / protein-protein complex / RBP / TTR / Amyloid / Disease mutation / Glycoprotein / Hormone / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Sensory transduction / Vision / TRANSPORT PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / vitamin A import into cell / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development ...Retinoid metabolism disease events / urinary bladder development / vitamin A import into cell / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / detection of light stimulus involved in visual perception / retinal metabolic process / molecular carrier activity / eye development / heart trabecula formation / retinal binding / retinol metabolic process / cardiac muscle tissue development / retinol binding / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / response to muscle activity / The canonical retinoid cycle in rods (twilight vision) / uterus development / hormone binding / vagina development / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / response to retinoic acid / retinoid metabolic process / Retinoid metabolism and transport / lung development / gluconeogenesis / response to insulin / hormone activity / positive regulation of insulin secretion / male gonad development / azurophil granule lumen / glucose homeostasis / heart development / response to ethanol / spermatogenesis / response to xenobiotic stimulus / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase ...Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 4 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsZanotti, G. / Cendron, L. / Gliubich, F. / Folli, C. / Berni, R.
Citation
Journal: Febs J. / Year: 2008
Title: Structural and mutational analyses of protein-protein interactions between transthyretin and retinol-binding protein.
Authors: Zanotti, G. / Folli, C. / Cendron, L. / Alfieri, B. / Nishida, S.K. / Gliubich, F. / Pasquato, N. / Negro, A. / Berni, R.
#1: Journal: Science / Year: 1995
Title: Structure of a complex of two plasma proteins: transthyretin and retinol-binding protein.
Authors: Monaco, H.L. / Rizzi, M. / Coda, A.
#2: Journal: Biochemistry / Year: 1999
Title: The structure of human retinol-binding protein (RBP) with its carrier protein transthyretin reveals an interaction with the carboxy terminus of RBP.
Authors: Naylor, H.M. / Newcomer, M.E.
#3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999
Title: Crystallization and preliminary X-ray data for the human transthyretin-retinol-binding protein (RBP) complex bound to an anti-RBP Fab.
Authors: Malpeli, G. / Zanotti, G. / Gliubich, F. / Rizzotto, A. / Nishida, S.K. / Folli, C. / Berni, R.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Nov 1, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Plasma retinol-binding protein
F: Plasma retinol-binding protein
L: Fab fragment heavy chain
H: Fab fragment light chain
M: Fab fragment heavy chain
N: Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,43112
Polymers188,85810
Non-polymers5732
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.620, 223.180, 121.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET11B-hTTR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Protein Plasma retinol-binding protein / PRBP / RBP


Mass: 20226.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: Plasma / References: UniProt: P02753

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Antibody , 2 types, 4 molecules LMHN

#3: Antibody Fab fragment heavy chain


Mass: 23708.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: A8P3 MAb
#4: Antibody Fab fragment light chain


Mass: 22939.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: A8P3 MAb

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Non-polymers , 2 types, 336 molecules

#5: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.35M ammonium phosphate, 10mM sodium citrate, 10mM beta-mercaptoethanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.3 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 21, 1997
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3.36→55 Å / Num. all: 25746 / Num. obs: 25746 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.3
Reflection shellResolution: 3.36→3.51 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1622 / % possible all: 77.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RBP, 1F41

1rbp

1f41


Resolution: 3.38→15.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 8281753.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1190 4.9 %RANDOM
Rwork0.239 ---
all0.241 25746 --
obs0.239 24044 78.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9765 Å2 / ksol: 0.32803 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1--16.97 Å20 Å20 Å2
2--8.37 Å20 Å2
3---8.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3.38→15.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13052 0 42 334 13428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.36→3.57 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 108 3.8 %
Rwork0.313 2760 -
obs--55.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x_ret.paramparam19x_ret.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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