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- PDB-9fse: Human ROR2 cysteine-rich domain (CRD) and Kringle domain -

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Basic information

Entry
Database: PDB / ID: 9fse
TitleHuman ROR2 cysteine-rich domain (CRD) and Kringle domain
ComponentsTyrosine-protein kinase transmembrane receptor ROR2
KeywordsSIGNALING PROTEIN / ROR2 / WNT / WNT5A / FRIZZLED / SIGNALLING / SECRETED / SIGNALLING PROTEIN / RECEPTOR TYROSINE KINASE / ROR
Function / homology
Function and homology information


regulation of synaptic signaling by nitric oxide / macrophage migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / positive regulation of macrophage differentiation / Wnt-protein binding / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization ...regulation of synaptic signaling by nitric oxide / macrophage migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / positive regulation of macrophage differentiation / Wnt-protein binding / male genitalia development / astrocyte development / mitogen-activated protein kinase kinase kinase binding / PCP/CE pathway / regulation of postsynapse organization / bone mineralization / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / clathrin-coated endocytic vesicle membrane / receptor protein-tyrosine kinase / Wnt signaling pathway / positive regulation of neuron projection development / postsynapse / microtubule / receptor complex / phosphorylation / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / dendrite / cell surface / signal transduction / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Kringle-like fold / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein kinase transmembrane receptor ROR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsGriffiths, S.C. / Tan, J. / Wagner, A. / Blazer, L.L. / Adams, J.J. / Srinivasan, S. / Moghisaei, S. / Sidhu, S.S. / Siebold, C. / Ho, H.H.
Funding support United Kingdom, United States, 8items
OrganizationGrant numberCountry
Cancer Research UKC20724/A26752 United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust099675/Z/12/Z United Kingdom
Cancer Research UKDRCRPG-May23/100002 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM144341 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2P30CA093373-19 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD018223 United States
CitationJournal: Elife / Year: 2024
Title: Structure and function of the ROR2 cysteine-rich domain in vertebrate noncanonical WNT5A signaling.
Authors: Griffiths, S.C. / Tan, J. / Wagner, A. / Blazer, L.L. / Adams, J.J. / Srinivasan, S. / Moghisaei, S. / Sidhu, S.S. / Siebold, C. / Ho, H.H.
History
DepositionJun 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase transmembrane receptor ROR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0464
Polymers26,7581
Non-polymers2883
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-34 kcal/mol
Surface area12640 Å2
Unit cell
Length a, b, c (Å)109.554, 109.554, 45.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Tyrosine-protein kinase transmembrane receptor ROR2 / Neurotrophic tyrosine kinase / receptor-related 2


Mass: 26758.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human ROR2 CRD and Kringle domains, expressed and secreted with C-terminal His-tag using the pHLsec vector for recombinant protein expression in mammalian cells
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR2, NTRKR2 / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q01974, receptor protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.5 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.48→94.88 Å / Num. obs: 7221 / % possible obs: 93.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 69.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Net I/σ(I): 14
Reflection shellResolution: 2.484→2.733 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 361 / CC1/2: 0.686 / Rpim(I) all: 0.429 / % possible all: 68.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC20230726data reduction
AutoSolphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.48→94.88 Å / SU ML: 0.1705 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 353 4.89 %Random
Rwork0.2365 6866 --
obs0.2381 7219 93.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.67 Å2
Refinement stepCycle: LAST / Resolution: 2.48→94.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 15 11 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00191799
X-RAY DIFFRACTIONf_angle_d0.46792437
X-RAY DIFFRACTIONf_chiral_restr0.0352249
X-RAY DIFFRACTIONf_plane_restr0.0041327
X-RAY DIFFRACTIONf_dihedral_angle_d11.5355674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.840.5803310.5695588X-RAY DIFFRACTION16.79
2.85-3.580.34151350.31762647X-RAY DIFFRACTION75.29
3.58-94.880.24111870.20453631X-RAY DIFFRACTION99.95
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)
19.57580384193-3.856850864460.4553059161231.902544386020.9300068610423.64979010761-0.0696628690566-1.13808955151.111999091971.09917632590.198005576155-0.618273279185-0.8905380908680.7611478750230.2974914657141.15593353850.140931760228-0.1662780768231.03411191635-0.09421658347690.029549118592-37.964110359932.720423083421.845699822
29.687997863842.033130895253.355657747276.040899952922.137551099974.49899639958-0.146535348912-1.399439900330.557806021905-0.02967251520870.02173250315920.647255455971-1.494931819280.211699804381-0.09581955419161.382425902230.0244070287146-0.1281508239360.681430406910.03075284293890.442871881781-38.213982776629.586807324220.0729966445
38.98282858472-4.78281188507-1.152584176943.49417768757-1.955767953897.15188588696-0.5536552836470.150589609548-0.44361783853-0.2333954855860.4851433920360.18347349094-0.426049332959-1.00967492542-0.03427907170580.456097411563-0.10985158902-0.01223386044530.311255356623-0.06348632624440.31474799192-46.973823356227.36172437998.49551985431
43.45154213616-1.43177107552-2.20826265436.26256056650.03114860118532.86382360452-0.270127791733-0.4593833708490.08872563783630.6510001008020.057287700108-0.9100145360120.09644374312241.267282746840.286720890920.453487857669-0.16482876561-0.1302733268660.597019770996-0.01750041877770.483906192217-30.59951299124.795570254410.5662431288
56.36049893019-3.316299830541.287792967083.64250573411-3.828433581915.41429523425-0.2107989437920.05528490085740.314787633877-0.2729697739940.155055873536-0.380462611820.372912890679-0.783196432434-0.005714199233910.507043273051-0.187258361966-0.0554444544960.471753223905-0.1233411423780.482658712722-45.305796239228.9524056238-1.3479959779
66.612228505380.703685035165-2.800222328962.186359657221.850657966714.59636899627-0.5452032636690.738549783955-1.22809577972-0.03231313988370.2804746700650.3119380850181.10451356048-0.7270478589640.2725685017530.652601615924-0.220701808904-0.08029469104540.523249456893-0.03359874437970.608442203738-30.49880735415.9296972945-0.367140171312
74.091991998432.42025062423-1.965358523614.65424558974-3.198570496823.86018140156-0.7814222971091.29520318682-0.984468742359-0.5510113582310.844119353653-0.02539238520411.23273727134-0.735746481966-0.05360163551160.504890154381-0.17451681002-0.03730315518980.7507465826-0.1551537388070.703042722258-21.184178584919.5773520087-15.2664827319
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 170 through 182 )170 - 1821 - 13
22chain 'A' and (resid 183 through 197 )183 - 19714 - 28
33chain 'A' and (resid 198 through 235 )198 - 23529 - 66
44chain 'A' and (resid 236 through 261 )236 - 26167 - 92
55chain 'A' and (resid 262 through 285 )262 - 28593 - 116
66chain 'A' and (resid 286 through 323 )286 - 323117 - 154
77chain 'A' and (resid 324 through 392 )324 - 392155 - 223

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