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- PDB-5cl1: Complex structure of Norrin with human Frizzled 4 -

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Basic information

Entry
Database: PDB / ID: 5cl1
TitleComplex structure of Norrin with human Frizzled 4
Components
  • Frizzled-4
  • Maltose-binding periplasmic protein,Norrin
KeywordsSIGNALING PROTEIN / Wnt / Norrin / Frizzled
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / progesterone secretion / retinal blood vessel morphogenesis / retinal rod cell differentiation ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / progesterone secretion / retinal blood vessel morphogenesis / retinal rod cell differentiation / locomotion involved in locomotory behavior / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / ubiquitin-dependent endocytosis / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 / retina layer formation / retinal pigment epithelium development / non-canonical Wnt signaling pathway / positive regulation of neuron projection arborization / establishment of blood-retinal barrier / Wnt receptor activity / glycine metabolic process / microglial cell proliferation / endothelial cell differentiation / dendritic spine development / Wnt-protein binding / establishment of blood-brain barrier / vacuole organization / protein targeting to lysosome / microglia differentiation / frizzled binding / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / positive regulation of dendrite morphogenesis / lens development in camera-type eye / exploration behavior / cytokine receptor activity / optic nerve development / action potential / smoothened signaling pathway / retinal ganglion cell axon guidance / cytokine binding / decidualization / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / response to axon injury / blood vessel remodeling / canonical Wnt signaling pathway / vasculogenesis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to retinoic acid / tricarboxylic acid cycle / Regulation of FZD by ubiquitination / visual perception / glutathione metabolic process / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cellular response to leukemia inhibitory factor / Asymmetric localization of PCP proteins / cytokine activity / G protein-coupled receptor activity / PDZ domain binding / sensory perception of sound / clathrin-coated endocytic vesicle membrane / neuron differentiation / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Ca2+ pathway / nervous system development / signaling receptor activity / mitotic cell cycle / amyloid-beta binding / cellular response to hypoxia / outer membrane-bounded periplasmic space / angiogenesis / neuron apoptotic process / collagen-containing extracellular matrix / cell population proliferation / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / protein ubiquitination / positive regulation of cell migration / inflammatory response / protein heterodimerization activity / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space / plasma membrane
Similarity search - Function
Norrie disease protein / Frizzled-4 / Frizzled 4, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Glycoprotein hormone subunit beta / Cystine-knot domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region ...Norrie disease protein / Frizzled-4 / Frizzled 4, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled cysteine-rich domain / Glycoprotein hormone subunit beta / Cystine-knot domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine-knot cytokine / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Norrin / Frizzled-4
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsWang, Z. / Ke, J. / Shen, G. / Cheng, Z. / Xu, H.E. / Xu, W.
CitationJournal: Cell Res. / Year: 2015
Title: Structural basis of the Norrin-Frizzled 4 interaction.
Authors: Shen, G. / Ke, J. / Wang, Z. / Cheng, Z. / Gu, X. / Wei, Y. / Melcher, K. / Xu, H.E. / Xu, W.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Norrin
B: Maltose-binding periplasmic protein,Norrin
C: Frizzled-4
D: Frizzled-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,4108
Polymers137,5254
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-39 kcal/mol
Surface area54600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.291, 150.589, 92.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA1 - 113311 - 483
21LYSLYSSERSERBB1 - 113311 - 483
12ARGARGMETMETCC44 - 15915 - 130
22ARGARGMETMETDD44 - 15915 - 130

NCS ensembles :
ID
1
2

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Components

#1: Protein Maltose-binding periplasmic protein,Norrin / MBP / MMBP / Maltodextrin-binding protein / Norrie disease protein / X-linked exudative ...MBP / MMBP / Maltodextrin-binding protein / Norrie disease protein / X-linked exudative vitreoretinopathy 2 protein


Mass: 53664.043 Da / Num. of mol.: 2 / Fragment: UNP Q00604 residues 31-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, NDP, EVR2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0AEY0, UniProt: Q00604
#2: Protein Frizzled-4 / hFz4 / FzE4


Mass: 15098.341 Da / Num. of mol.: 2 / Fragment: UNP residues 38-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9ULV1
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM ammonium sulfate, 100 mM sodium cacodylate trihydrate (pH 6.5), 15% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2015
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 18303 / % possible obs: 90.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.264 / Rpim(I) all: 0.117 / Rrim(I) all: 0.28 / Χ2: 1.123 / Net I/av σ(I): 4.476 / Net I/σ(I): 3.5 / Num. measured all: 107966
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.8-3.913.30.92310840.9230.5260.97865.2
3.91-4.043.812090.4750.5330.97773.1
4.04-4.184.10.77513110.5730.3881.03680.10.874
4.18-4.354.40.57713960.7630.2771.08485.10.645
4.35-4.554.70.4914970.7810.2341.20188.90.547
4.55-4.795.10.41315610.8630.1911.17394.20.458
4.79-5.095.80.43616330.8530.1921.133980.48
5.09-5.486.60.4816800.850.2011.11999.70.522
5.48-6.037.70.55516740.8670.2161.0681000.596
6.03-6.97.90.39817080.9270.1521.1121000.427
6.9-8.697.70.20817240.9850.081.2431000.223
8.69-507.40.0918260.9970.0351.11999.90.097

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MY2

4my2


Resolution: 3.8→50 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.808 / SU B: 144.371 / SU ML: 0.843 / Cross valid method: THROUGHOUT / ESU R Free: 0.905 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3105 889 4.9 %RANDOM
Rwork0.2615 ---
obs0.2639 17383 89.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.82 Å2 / Biso mean: 112.326 Å2 / Biso min: 71.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 3.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9171 0 56 0 9227
Biso mean--143.79 --
Num. residues----1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0199464
X-RAY DIFFRACTIONr_bond_other_d0.0010.028936
X-RAY DIFFRACTIONr_angle_refined_deg0.771.9712827
X-RAY DIFFRACTIONr_angle_other_deg0.661320665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.15751171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.75224.729406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.859151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3221541
X-RAY DIFFRACTIONr_chiral_restr0.0460.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02110604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022065
X-RAY DIFFRACTIONr_mcbond_it1.4538.7074702
X-RAY DIFFRACTIONr_mcbond_other1.4538.7084701
X-RAY DIFFRACTIONr_mcangle_it2.65213.0585867
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27920.08
12B27920.08
21C6890.04
22D6890.04
LS refinement shellResolution: 3.8→3.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 38 -
Rwork0.399 810 -
all-848 -
obs--57.3 %
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)
10.2218-0.0078-0.23420.00140.01320.47790.0421-0.00050.04720.00270.01740.0002-0.04270.0651-0.05950.1133-0.01830.00350.6243-0.00620.025517.679147.1153120.7356
21.0331-0.02710.41010.05880.11150.45680.0639-0.1328-0.1367-0.01290.0184-0.00120.08780.0149-0.08230.20540.0362-0.04670.62080.04170.028223.823734.540267.1489
30.31480.9231-0.44224.1897-0.28541.668-0.05190.09030.1132-0.43350.01030.3786-0.2423-0.1430.04160.1180.0792-0.08750.62590.06590.12736.111355.625661.6009
40.8554-0.432-0.81133.9310.0131.09230.1036-0.20820.11390.09370.19510.0534-0.0480.1653-0.29860.07190.0606-0.00170.4830.00650.150336.679536.4811118.4161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1133
2X-RAY DIFFRACTION2B1 - 1133
3X-RAY DIFFRACTION3C44 - 160
4X-RAY DIFFRACTION4D43 - 160

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