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- PDB-6wbh: Crystal structure of mRECK(CC4) in fusion with engineered MBP at ... -

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Basic information

Entry
Database: PDB / ID: 6wbh
TitleCrystal structure of mRECK(CC4) in fusion with engineered MBP at medium resolution
ComponentsMaltodextrin-binding protein,Reversion-inducing cysteine-rich protein with Kazal motifs fusion
KeywordsSIGNALING PROTEIN / Wnt signaling / 4-helix bundle / extracellular domain / vascularization / blood-brain barrier / Maltose-binding protein
Function / homology
Function and homology information


regulation of establishment of blood-brain barrier / : / negative regulation of metalloendopeptidase activity / Post-translational modification: synthesis of GPI-anchored proteins / blood vessel maturation / : / metalloendopeptidase inhibitor activity / Wnt-protein binding / embryonic forelimb morphogenesis / Wnt signalosome ...regulation of establishment of blood-brain barrier / : / negative regulation of metalloendopeptidase activity / Post-translational modification: synthesis of GPI-anchored proteins / blood vessel maturation / : / metalloendopeptidase inhibitor activity / Wnt-protein binding / embryonic forelimb morphogenesis / Wnt signalosome / sprouting angiogenesis / endopeptidase inhibitor activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / regulation of angiogenesis / embryo implantation / ATP-binding cassette (ABC) transporter complex / extracellular matrix organization / cell chemotaxis / negative regulation of cell migration / serine-type endopeptidase inhibitor activity / positive regulation of canonical Wnt signaling pathway / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / plasma membrane
Similarity search - Function
Reversion-inducing cysteine-rich protein with Kazal motifs / Kazal-type serine protease inhibitor domain / Kazal serine protease inhibitors family signature. / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Reversion-inducing cysteine-rich protein with Kazal motifs / Kazal-type serine protease inhibitor domain / Kazal serine protease inhibitors family signature. / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / 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 / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / Reversion-inducing cysteine-rich protein with Kazal motifs
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.455 Å
Model detailsmouse RECK CC domain 4 in fusion with engineered Maltose Binding Protein at medium resolution
AuthorsChang, T.H. / Hsieh, F.L. / Gabelli, S.B. / Nathans, J.
Funding support United States, France, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY018637 United States
Howard Hughes Medical Institute (HHMI) United States
Human Frontier Science Program (HFSP)LT000130/2017-L France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of the RECK CC domain, an evolutionary anomaly.
Authors: Chang, T.H. / Hsieh, F.L. / Smallwood, P.M. / Gabelli, S.B. / Nathans, J.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / 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_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / 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 / _atom_site.type_symbol / _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 / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / 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_audit_support / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Reversion-inducing cysteine-rich protein with Kazal motifs fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6055
Polymers49,0961
Non-polymers5094
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.222, 110.599, 57.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Maltodextrin-binding protein,Reversion-inducing cysteine-rich protein with Kazal motifs fusion / mRECK


Mass: 49096.473 Da / Num. of mol.: 1
Mutation: D84A,K85A,E174A,N175A,A217H,K221H,K241A,A314V,I319V,E361A,K364A,D365A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Mus musculus (house mouse)
Gene: malE, DJ492_13065, EPS91_05465, FV295_14110, NCTC8450_00456, Reck
Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle (DE3)
References: UniProt: A0A376KDN7, UniProt: Q9Z0J1, UniProt: P0AEX9*PLUS
#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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.89 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.45→45.53 Å / Num. obs: 19054 / % possible obs: 98.3 % / Redundancy: 6.3 % / CC1/2: 0.947 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.081 / Rrim(I) all: 0.208 / Net I/σ(I): 7.4
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.511 / Num. unique obs: 1811 / CC1/2: 0.837 / Rpim(I) all: 0.222 / Rrim(I) all: 0.562 / % possible all: 94.52

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.78 Å45.53 Å
Translation5.78 Å45.53 Å

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHASER2.8.1phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SET

3set


Resolution: 2.455→45.53 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.12
RfactorNum. reflection% reflection
Rfree0.2196 932 4.9 %
Rwork0.1944 --
obs0.1957 19015 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.3 Å2 / Biso mean: 23.4561 Å2 / Biso min: 6.49 Å2
Refinement stepCycle: final / Resolution: 2.455→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 47 219 3588
Biso mean--17.83 25.35 -
Num. residues----431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.455-2.580.28051510.2383242394
2.5839-2.74580.23221060.211253797
2.7458-2.95770.2311180.2236252397
2.9577-3.25530.22681430.1938254598
3.2553-3.72620.21351370.1779261099
3.7262-4.69380.1971370.1737265299
4.6938-45.530.2011400.18962793100
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)
10.8169-0.0267-0.36581.140.17990.77320.06520.01350.1444-0.2563-0.08170.1685-0.1914-0.20550.00980.16360.0341-0.00990.16220.02180.1518-9.956740.9864-19.4219
20.4720.0130.13690.78620.00840.40220.0301-0.0909-0.03450.0498-0.0308-0.1650.0240.2404-0.00020.11860.04650.0060.10610.01830.08620.634727.3499-11.6821
30.8204-0.1682-0.12460.88530.28471.10390.0642-0.0054-0.1033-0.027-0.09310.03690.0104-0.08920.04450.1139-0.00050.00240.09510.00620.1238-12.071613.8971-10.6793
40.60620.0449-0.12530.62330.09840.24940.02980.0233-0.0332-0.13340.0123-0.0147-0.01610.0042-0.02160.12220.0246-0.00120.11830.0260.1022-2.664128.6799-12.5622
51.33492.1842-0.55863.5748-0.91720.2252-0.20470.13160.0612-0.70430.21380.20650.2290.0345-0.17780.29610.024-0.05360.2661-0.07230.1893-3.916223.3378-35.6988
61.6997-0.1674-0.05461.1807-0.01271.48490.1427-0.24250.04120.1186-0.08830.1178-0.14890.0592-0.01380.20820.0005-0.00180.2513-0.04790.16411.228540.3538-48.0195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 75 )A4 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 133 )A76 - 133
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 247 )A134 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 354 )A248 - 354
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 389 )A355 - 389
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 434 )A390 - 434

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