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- PDB-1rlb: RETINOL BINDING PROTEIN COMPLEXED WITH TRANSTHYRETIN -

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Basic information

Entry
Database: PDB / ID: 1rlb
TitleRETINOL BINDING PROTEIN COMPLEXED WITH TRANSTHYRETIN
Components
  • RETINOL BINDING PROTEIN
  • TRANSTHYRETIN
KeywordsCOMPLEX (PROTEIN/PROTEIN) / COMPLEX (PROTEIN-PROTEIN) / COMPLEX (PROTEIN-PROTEIN) 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
RETINOIC ACID / Retinol-binding protein 4 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsMonaco, H.L. / Rizzi, M. / Coda, A.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of the Macromolecular Complex Transthyretin Retinol Binding Protein
Authors: Monaco, H.L. / Mancia, F. / Rizzi, M. / Coda, A.
History
DepositionFeb 20, 1995Processing site: BNL
Revision 1.0Apr 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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: RETINOL BINDING PROTEIN
F: RETINOL BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8658
Polymers95,2656
Non-polymers6012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-60 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.400, 163.400, 55.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
TRANSTHYRETIN / PREALBUMIN


Mass: 13776.376 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / References: UniProt: P02766
#2: Protein RETINOL BINDING PROTEIN


Mass: 20079.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: PLASMA / References: UniProt: P02753
#3: Chemical ChemComp-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2
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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal
*PLUS
Density % sol: 53.5 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein11
20.1 Msuccinate12
33 %ethylene glycol12
42.3 Mammonium sulfate12

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 17465 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 6 Å / Num. measured all: 47491 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.3 Å / % possible obs: 83.2 % / Num. unique obs: 2359

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Processing

Software
NameClassification
MSCdata collection
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
X-PLORphasing
RefinementResolution: 3.1→6 Å / σ(F): 0
Details: THERE IS CLOSE CONTACT BETWEEN RESIDUE GLU D 66 AND A SYMMETRY-RELATED COPY OF ITSELF.
RfactorNum. reflection% reflection
Rwork0.215 --
obs0.215 14891 93.5 %
Refinement stepCycle: LAST / Resolution: 3.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 42 0 6624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 26.7

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