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- PDB-4my2: Crystal Structure of Norrin in fusion with Maltose Binding Protein -

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Basic information

Entry
Database: PDB / ID: 4my2
TitleCrystal Structure of Norrin in fusion with Maltose Binding Protein
ComponentsMaltose-binding periplasmic protein, Norrin fusion protein
KeywordsSIGNALING PROTEIN / Cystine-knot growth factor / Wnt signaling / Cysteine-rich protein / Angiogenesis / Eye development / Wnt/beta-catenin signaling / Frizzled 4 receptor / Lrp5/6 / extracellular / fusion protein
Function / homology
Function and homology information


retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / ubiquitin-dependent endocytosis / retina layer formation / retinal pigment epithelium development ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / ubiquitin-dependent endocytosis / retina layer formation / retinal pigment epithelium development / establishment of blood-retinal barrier / glycine metabolic process / microglial cell proliferation / endothelial cell differentiation / dendritic spine development / establishment of blood-brain barrier / vacuole organization / protein targeting to lysosome / microglia differentiation / frizzled binding / lens development in camera-type eye / exploration behavior / optic nerve development / action potential / smoothened signaling pathway / retinal ganglion cell axon guidance / decidualization / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / response to axon injury / blood vessel remodeling / canonical Wnt signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / tricarboxylic acid cycle / visual perception / glutathione metabolic process / transforming growth factor beta receptor signaling pathway / cytokine activity / nervous system development / mitotic cell cycle / cellular response to hypoxia / outer membrane-bounded periplasmic space / angiogenesis / neuron apoptotic process / collagen-containing extracellular matrix / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / inflammatory response / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space
Similarity search - Function
Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine-knot cytokine / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...Norrie disease protein / Glycoprotein hormone subunit beta / Cystine-knot domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine-knot cytokine / 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
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Norrin
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKe, J. / Jurecky, C. / Chen, C. / Gu, X. / Parker, N. / Williams, B.O. / Melcher, K. / Xu, H.E.
CitationJournal: Genes Dev. / Year: 2013
Title: Structure and function of Norrin in assembly and activation of a Frizzled 4-Lrp5/6 complex.
Authors: Ke, J. / Harikumar, K.G. / Erice, C. / Chen, C. / Gu, X. / Wang, L. / Parker, N. / Cheng, Z. / Xu, W. / Williams, B.O. / Melcher, K. / Miller, L.J. / Xu, H.E.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Norrin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1772
Polymers52,8351
Non-polymers3421
Water3,351186
1
A: Maltose-binding periplasmic protein, Norrin fusion protein
hetero molecules

A: Maltose-binding periplasmic protein, Norrin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3554
Polymers105,6702
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area3690 Å2
ΔGint-23 kcal/mol
Surface area42620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.458, 79.022, 104.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1362-

HOH

21A-1390-

HOH

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Components

#1: Protein Maltose-binding periplasmic protein, Norrin fusion protein / 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: 52835.168 Da / Num. of mol.: 1
Fragment: Maltose binding protein (UNP residues 26-392), Norrin (UNP residues 30-133) fusion protein
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 / Plasmid: pETDUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: P0AEY0, UniProt: Q00604
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 3350, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2011
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 19865 / Num. obs: 19865 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 13.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 9 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 3 / Num. unique all: 2831 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C4M

3c4m


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.236 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1015 5.1 %RANDOM
Rwork0.20657 ---
all0.2082 18844 --
obs0.20816 18833 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.6 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 23 186 3897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.023805
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9695157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54624.756164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0515646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1941516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212864
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 70 -
Rwork0.314 1244 -
obs--99.92 %

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