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- PDB-3u9u: Crystal Structure of Extracellular Domain of Human ErbB4/Her4 in ... -

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Basic information

Entry
Database: PDB / ID: 3u9u
TitleCrystal Structure of Extracellular Domain of Human ErbB4/Her4 in complex with the Fab fragment of mAb1479
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Receptor tyrosine-protein kinase erbB-4
KeywordsTRANSFERASE / Cell Surface Receptor / Tyrosine Kinase Receptor
Function / homology
Function and homology information


establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / negative regulation of neuron migration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process ...establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / negative regulation of neuron migration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / mammary gland epithelial cell differentiation / PI3K events in ERBB4 signaling / embryonic pattern specification / GABA receptor binding / positive regulation of protein localization to cell surface / neural crest cell migration / epidermal growth factor receptor binding / epidermal growth factor receptor activity / positive regulation of tyrosine phosphorylation of STAT protein / ERBB2 Activates PTK6 Signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / ERBB2 Regulates Cell Motility / Signaling by ERBB4 / PI3K events in ERBB2 signaling / Long-term potentiation / mammary gland alveolus development / SHC1 events in ERBB4 signaling / cell fate commitment / cell surface receptor signaling pathway via JAK-STAT / Nuclear signaling by ERBB4 / positive regulation of cardiac muscle cell proliferation / synapse assembly / lactation / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / Downregulation of ERBB4 signaling / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell migration / basal plasma membrane / cellular response to epidermal growth factor stimulus / peptidyl-tyrosine phosphorylation / positive regulation of epithelial cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / postsynaptic density membrane / GABA-ergic synapse / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / nervous system development / PIP3 activates AKT signaling / heart development / protein autophosphorylation / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / basolateral plasma membrane / Estrogen-dependent gene expression / postsynaptic membrane / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / transcription cis-regulatory region binding / positive regulation of MAPK cascade / mitochondrial matrix / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / glutamatergic synapse / signal transduction / protein homodimerization activity / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV ...Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Alpha-Beta Horseshoe / 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 / : / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsHollmen, M. / Liu, P. / Wildiers, H. / Reinvall, I. / Vandorpe, T. / Smeets, A. / Deraedt, K. / Vahlberg, T. / Joensuu, H. / Leahy, D.J. ...Hollmen, M. / Liu, P. / Wildiers, H. / Reinvall, I. / Vandorpe, T. / Smeets, A. / Deraedt, K. / Vahlberg, T. / Joensuu, H. / Leahy, D.J. / Schoffski, P. / Elenius, K.
CitationJournal: Plos One / Year: 2012
Title: Proteolytic processing of ErbB4 in breast cancer.
Authors: Hollmen, M. / Liu, P. / Kurppa, K. / Wildiers, H. / Reinvall, I. / Vandorpe, T. / Smeets, A. / Deraedt, K. / Vahlberg, T. / Joensuu, H. / Leahy, D.J. / Schoffski, P. / Elenius, K.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 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: Fab Heavy Chain
B: Fab Light Chain
C: Fab Heavy Chain
D: Fab Light Chain
E: Receptor tyrosine-protein kinase erbB-4
F: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)236,5376
Polymers236,5376
Non-polymers00
Water00
1
A: Fab Heavy Chain
B: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,4012
Polymers48,4012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-29 kcal/mol
Surface area19720 Å2
MethodPISA
2
C: Fab Heavy Chain
D: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,4012
Polymers48,4012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-30 kcal/mol
Surface area19320 Å2
MethodPISA
3
E: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)69,8681
Polymers69,8681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)69,8681
Polymers69,8681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.121, 110.914, 362.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab Heavy Chain


Mass: 24195.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Hybridoma Cells / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Production host: Mus musculus (house mouse)
#2: Antibody Fab Light Chain


Mass: 24205.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Hybridoma Cells / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Production host: Mus musculus (house mouse)
#3: Protein Receptor tyrosine-protein kinase erbB-4 / Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 ...Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 / ERBB4 intracellular domain / 4ICD / E4ICD / s80HER4


Mass: 69867.766 Da / Num. of mol.: 2 / Fragment: Extracellular region 1-625, JM-a isoform
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Plasmid: PSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO (Lec1)
References: UniProt: Q15303, receptor protein-tyrosine kinase
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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG4000, 0.2 M Sodium Acetate, 0.1 M Sodium Citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2010
RadiationMonochromator: Doulbe Crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 44255 / Num. obs: 44255 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 73.77 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.4-3.522.30.612195.8
3.52-3.662.50.502197.6
3.66-3.832.80.411197.9
3.83-4.032.90.317197.7
4.03-4.2830.229197.4
4.28-4.6130.154196.3
4.61-5.0830.118196.3
5.08-5.8130.113194.7
5.81-7.323.10.083193.3
7.32-5030.042186.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHX, 1N8Z

2ahx

1n8z


Resolution: 3.42→45.26 Å / Cor.coef. Fo:Fc: 0.831 / Cor.coef. Fo:Fc free: 0.7841 / Occupancy max: 1 / Occupancy min: 0.51 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 2230 5.05 %RANDOM
Rwork0.2341 ---
obs0.236 44127 95.26 %-
all-44127 --
Displacement parametersBiso mean: 112.38 Å2
Baniso -1Baniso -2Baniso -3
1--64.2676 Å20 Å20 Å2
2--34.444 Å20 Å2
3---29.8236 Å2
Refine analyzeLuzzati coordinate error obs: 0.864 Å
Refinement stepCycle: LAST / Resolution: 3.42→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15819 0 0 0 15819
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00916230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1622070HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5460SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes398HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2345HARMONIC5
X-RAY DIFFRACTIONt_it16230HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact
LS refinement shellResolution: 3.42→3.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2919 183 5.71 %
Rwork0.2574 3020 -
all0.2593 3203 -
obs--95.26 %
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)
10.1561-0.29990.19032.61870.90892.8439-0.013-0.04790.1494-0.19790.01560.03420.0547-0.0172-0.00260.1130.0157-0.0093-0.18260.0113-0.08-17.334517.623130.2094
20.4738-1.0522-0.83062.78551.37190.95830.0048-0.02420.126-0.03810.02280.19310.1433-0.0399-0.02750.0801-0.0034-0.1073-0.16760.00960.0724-28.83877.840739.6063
30.25240.2030.10473.1046-1.27920.6276-0.0215-0.03180.0356-0.05930.0260.1017-0.05110.0347-0.00450.01760.0325-0.0588-0.0857-0.02010.0061-18.2832-38.37542.5255
40.59320.6586-1.21141.0546-1.59382.06380.01160.00870.0048-0.13330.059-0.12180.06940.1023-0.07060.12970.0498-0.0177-0.115-0.0068-0.0491-6.2572-47.600432.8577
500.2844-0.09820.91551.03060.240.08190.0382-0.12790.1495-0.0013-0.0680.0955-0.0713-0.0806-0.15480.1469-0.00570.0584-0.08220.001121.2652-20.677.1798
60.2341-0.19010.49431.3479-1.1670.6544-0.02590.2634-0.0770.25820.02910.05360.0319-0.0686-0.00320.05140.0234-0.0071-0.0119-0.1085-0.1343-18.618-19.88-31.9436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|224 }A1 - 224
2X-RAY DIFFRACTION2{ B|1 - B|219 }B1 - 219
3X-RAY DIFFRACTION3{ C|1 - C|220 }C1 - 220
4X-RAY DIFFRACTION4{ D|1 - D|219 }D1 - 219
5X-RAY DIFFRACTION5{ E|2 - E|612 }E2 - 612
6X-RAY DIFFRACTION6{ F|2 - F|611 }F2 - 611

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