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- PDB-7bhe: DARPin_D5/Her3 domain 4 complex, monoclinic crystals -

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Basic information

Entry
Database: PDB / ID: 7bhe
TitleDARPin_D5/Her3 domain 4 complex, monoclinic crystals
Components
  • DARPin_D5
  • Receptor tyrosine-protein kinase erbB-3
KeywordsPROTEIN BINDING / designed ankyrin repeat protein
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / growth factor binding / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / Schwann cell development / negative regulation of signal transduction / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / myelination / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / neurogenesis / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / heart development / regulation of cell population proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / apical plasma membrane / protein heterodimerization activity / phosphorylation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats ...Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.297 Å
AuthorsMittl, P.R.E. / Radom, F. / Pluckthun, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of HER3 extracellular domain 4 in complex with the designed ankyrin-repeat protein D5.
Authors: Radom, F. / Vonrhein, C. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DARPin_D5
B: Receptor tyrosine-protein kinase erbB-3
C: DARPin_D5
D: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,55110
Polymers62,0974
Non-polymers4536
Water8,341463
1
A: DARPin_D5
B: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4107
Polymers31,0492
Non-polymers3615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-11 kcal/mol
Surface area12970 Å2
MethodPISA
2
C: DARPin_D5
D: Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1413
Polymers31,0492
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-9 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.872, 62.254, 74.545
Angle α, β, γ (deg.)90.000, 102.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DARPin_D5


Mass: 14908.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 16140.108 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21860, receptor protein-tyrosine kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.83 / Details: 0.1 M Na citrate, 12% PEG4000, 0.2 M Li sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.296→44.405 Å / Num. obs: 24338 / % possible obs: 93.2 % / Redundancy: 4.52 % / Biso Wilson estimate: 37.85 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.063 / Rrim(I) all: 0.147 / Net I/σ(I): 5.4
Reflection shellResolution: 2.296→2.336 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1250 / CC1/2: 0.84 / Rpim(I) all: 0.249 / Rrim(I) all: 0.576 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (11-DEC-2020)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2y0b

2y0b


Resolution: 2.297→44.4 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.409 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 1185 4.87 %RANDOM
Rwork0.184 ---
obs0.1873 24338 93.2 %-
Displacement parametersBiso max: 80.65 Å2 / Biso mean: 34.4 Å2 / Biso min: 11.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.5187 Å20 Å22.3119 Å2
2--8.4759 Å20 Å2
3----10.9946 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.297→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 30 463 4311
Biso mean--54.05 38.31 -
Num. residues----514
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1318SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes706HARMONIC5
X-RAY DIFFRACTIONt_it3953HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3523SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3953HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5368HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion16.74
LS refinement shellResolution: 2.3→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2928 24 4.93 %
Rwork0.2307 463 -
all0.2336 487 -
obs--94.36 %
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)
11.3101-0.9424-0.98272.40.78474.03380.03110.05740.016-0.0188-0.1397-0.08510.0541-0.02440.1085-0.1436-0.0214-0.0146-0.23450.0185-0.1023-6.0038-30.8002-0.0614
22.6304-0.6430.18311.94110.51031.6920.0010.35630.0743-0.00240.0867-0.03140.06820.0703-0.0877-0.1610.0355-0.0621-0.22360.0164-0.22583.9882-22.6207-20.0432
31.0358-1.15091.09072.563-0.97771.9831-0.4575-0.2690.28040.5340.0415-0.0054-0.9489-0.29740.4160.61680.1244-0.22910.1623-0.15860.417926.6037-17.05580.1764
40.9121-0.2182-0.42621.00130.52671.0750.2322-0.32110.36880.29630.1878-0.311-0.19620.4577-0.420.4861-0.18410.08660.2442-0.09530.354436.6056-24.984920.0728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A11 - 136
2X-RAY DIFFRACTION2{ B|* }B481 - 611
3X-RAY DIFFRACTION3{ C|* }C11 - 136
4X-RAY DIFFRACTION4{ D|* }D481 - 611

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