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- PDB-4i18: Crystal structure of human prolactin receptor complexed with Fab ... -

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Basic information

Entry
Database: PDB / ID: 4i18
TitleCrystal structure of human prolactin receptor complexed with Fab fragment
Components
  • Prolactin receptor
  • antibody heavy chainImmunoglobulin heavy chain
  • antibody light chainImmunoglobulin light chain
KeywordsCYTOKINE / SIGNALING PROTEIN / immunoglobulin fold / prolactin binding / receptor signaling
Function / homology
Function and homology information


prolactin receptor activity / regulation of epithelial cell differentiation / prostate gland growth / mammary gland epithelial cell differentiation / steroid biosynthetic process / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / activation of transmembrane receptor protein tyrosine kinase activity / cytokine binding / Prolactin receptor signaling ...prolactin receptor activity / regulation of epithelial cell differentiation / prostate gland growth / mammary gland epithelial cell differentiation / steroid biosynthetic process / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / activation of transmembrane receptor protein tyrosine kinase activity / cytokine binding / Prolactin receptor signaling / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / mammary gland alveolus development / regulation of cell adhesion / positive regulation of B cell proliferation / Growth hormone receptor signaling / embryo implantation / positive regulation of protein autophosphorylation / lactation / endosome lumen / response to bacterium / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / receptor complex / external side of plasma membrane / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold ...Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Prolactin receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.238 Å
AuthorsDuguid, E.M. / Mukherjee, S. / Kouadio, J.L.
CitationJournal: Cell Commun Signal / Year: 2015
Title: Engineering synthetic antibody binders for allosteric inhibition of prolactin receptor signaling.
Authors: Rizk, S.S. / Kouadio, J.L. / Szymborska, A. / Duguid, E.M. / Mukherjee, S. / Zheng, J. / Clevenger, C.V. / Kossiakoff, A.A.
History
DepositionNov 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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
L: antibody light chain
H: antibody heavy chain
B: antibody light chain
A: antibody heavy chain
R: Prolactin receptor
C: Prolactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,48813
Polymers146,9806
Non-polymers5087
Water0
1
L: antibody light chain
H: antibody heavy chain
C: Prolactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8067
Polymers73,4903
Non-polymers3164
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-41 kcal/mol
Surface area27720 Å2
MethodPISA
2
B: antibody light chain
A: antibody heavy chain
R: Prolactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6816
Polymers73,4903
Non-polymers1913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-54 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.826, 285.826, 62.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21B
12H
22A
/ NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules RC

#3: Protein Prolactin receptor / / PRL-R


Mass: 24543.875 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 25-235)
Source method: isolated from a genetically manipulated source
Details: Periplasmic expression / Source: (gene. exp.) Homo sapiens (human) / Gene: PRLR / Production host: Escherichia coli (E. coli) / References: UniProt: P16471

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Antibody , 2 types, 4 molecules LBHA

#1: Antibody antibody light chain / Immunoglobulin light chain


Mass: 23873.432 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Details: Periplasmic expression under phoA promoter / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 55244
#2: Antibody antibody heavy chain / Immunoglobulin heavy chain


Mass: 25072.812 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Details: Periplasmic expression under phoA promoter / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 55244

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Non-polymers , 3 types, 7 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

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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: 4.99 Å3/Da / Density % sol: 75.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 160 mM calcium acetate, 80 mM sodium cacodylate, pH 6.2, 11% PEG8000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 23, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.238→250 Å / Num. all: 47796 / Num. obs: 47509 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.207 / Χ2: 1.566 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.238-3.374.30.7545841.261197.8
3.37-3.55.30.65347291.333199.7
3.5-3.6660.51647361.49199.9
3.66-3.856.50.44247081.556199.8
3.85-4.096.80.3447571.572199.8
4.09-4.416.90.20447471.625199.8
4.41-4.856.90.16247692.015199.5
4.85-5.567.10.13647551.65199.7
5.56-77.40.12548061.426199.2
7-507.30.05949181.533198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2R8S AND 3D48

2r8s

3d48


Resolution: 3.238→49.507 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.2217 / WRfactor Rwork: 0.1715 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.858 / SU B: 34.491 / SU ML: 0.262 / SU R Cruickshank DPI: 0.9116 / SU Rfree: 0.3841 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.912 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT, ANISOU RECORDS REMOVED BY AUTHOR REQUEST
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 2365 5.1 %RANDOM
Rwork0.1912 ---
obs0.1939 46730 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.04 Å2 / Biso mean: 59.658 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.85 Å2-0 Å2
2--1.69 Å2-0 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 3.238→49.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9873 0 30 0 9903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0210191
X-RAY DIFFRACTIONr_angle_refined_deg2.1381.94513885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.48451259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22223.923418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.205151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1181537
X-RAY DIFFRACTIONr_chiral_restr0.1340.21502
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217764
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L750MEDIUM POSITIONAL0.090.5
1L804TIGHT THERMAL8.840.5
1L750MEDIUM THERMAL8.942
2H689MEDIUM POSITIONAL0.130.5
2H801TIGHT THERMAL6.070.5
2H689MEDIUM THERMAL6.592
LS refinement shellResolution: 3.238→3.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 158 -
Rwork0.284 3031 -
all-3189 -
obs--96.64 %
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)
10.1416-0.0618-0.13722.845-0.27590.7302-0.07390.0430.0603-0.07850.22890.3964-0.0275-0.2175-0.1550.1602-0.0342-0.08510.08990.06290.1801-157.3303-16.0977-17.7393
20.2340.26090.11281.5711-0.10971.2706-0.0850.01270.0431-0.23140.14750.1699-0.0452-0.13-0.06250.1378-0.02420.00650.04030.00050.1116-144.8502-24.7234-8.2044
31.2046-0.02570.21162.2002-1.24342.5486-0.1654-0.0370.3790.2429-0.153-0.7311-0.37440.71110.31840.0859-0.0875-0.09850.2372-0.00410.4226-101.7038-19.96786.7179
40.5371-0.00870.16740.9683-0.66851.0856-0.0590.11440.06240.0289-0.0174-0.10120.05310.17740.07640.14910.00190.05530.0611-0.00170.0713-117.6431-27.6811.1387
51.1676-0.3751-2.46781.16040.62886.69590.0341-0.0514-0.059-0.0393-0.1073-0.16160.47370.34270.07310.28780.1367-0.00750.08870.00650.1164-115.7048-59.886423.5513
62.84390.8674-1.11581.4690.39085.5143-0.16730.1286-0.14060.06160.2257-0.10690.46050.0632-0.05840.2851-0.137-0.02410.1235-0.00530.1437-157.0219-60.1505-17.1508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 216
2X-RAY DIFFRACTION2H4 - 230
3X-RAY DIFFRACTION3B1 - 215
4X-RAY DIFFRACTION4A4 - 228
5X-RAY DIFFRACTION5R3 - 211
6X-RAY DIFFRACTION6C3 - 201

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