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- PDB-8e0p: Crystal structure of mouse APCDD1 in fusion with engineered MBP -

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Basic information

Entry
Database: PDB / ID: 8e0p
TitleCrystal structure of mouse APCDD1 in fusion with engineered MBP
ComponentsMaltodextrin-binding protein, Protein APCDD1 complex
KeywordsSIGNALING PROTEIN / cell signaling protein / beta barrel / lipid binding protein
Function / homology
Function and homology information


regulation of odontogenesis of dentin-containing tooth / astrocyte cell migration / Wnt-protein binding / negative regulation of Wnt signaling pathway / carbohydrate transmembrane transporter activity / hair follicle development / Wnt signaling pathway / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane
Similarity search - Function
APCDD1 domain / Protein APCDD1 / Adenomatosis polyposis coli down-regulated 1 / Adenomatosis polyposis coli down-regulated 1 / 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
3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE / PALMITIC ACID / Maltodextrin-binding protein / Protein APCDD1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsHsieh, F.L. / Chang, T.H. / Gabelli, S.B. / Nathans, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein.
Authors: Hsieh, F.L. / Chang, T.H. / Gabelli, S.B. / Nathans, J.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein, Protein APCDD1 complex
B: Maltodextrin-binding protein, Protein APCDD1 complex
C: Maltodextrin-binding protein, Protein APCDD1 complex
D: Maltodextrin-binding protein, Protein APCDD1 complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,50933
Polymers366,6334
Non-polymers5,87529
Water11,584643
1
A: Maltodextrin-binding protein, Protein APCDD1 complex
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 93 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)93,0488
Polymers91,6581
Non-polymers1,3907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein, Protein APCDD1 complex
hetero molecules


  • defined by author
  • 92.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)92,8848
Polymers91,6581
Non-polymers1,2267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltodextrin-binding protein, Protein APCDD1 complex
hetero molecules


  • defined by author
  • 93.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)93,5279
Polymers91,6581
Non-polymers1,8698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltodextrin-binding protein, Protein APCDD1 complex
hetero molecules


  • defined by author
  • 93 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)93,0498
Polymers91,6581
Non-polymers1,3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.914, 98.361, 156.513
Angle α, β, γ (deg.)90.000, 109.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 57 or resid 59...
21(chain B and (resid 1 through 57 or resid 59...
31(chain C and (resid 1 through 2 or resid 8...
41(chain D and (resid 1 through 2 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 57 or resid 59...A1 - 57
121(chain A and (resid 1 through 57 or resid 59...A59 - 379
131(chain A and (resid 1 through 57 or resid 59...A381 - 386
141(chain A and (resid 1 through 57 or resid 59...A388 - 451
151(chain A and (resid 1 through 57 or resid 59...A8 - 795
161(chain A and (resid 1 through 57 or resid 59...A470
171(chain A and (resid 1 through 57 or resid 59...A8 - 795
181(chain A and (resid 1 through 57 or resid 59...A8 - 795
191(chain A and (resid 1 through 57 or resid 59...A696 - 732
1101(chain A and (resid 1 through 57 or resid 59...A8 - 795
1111(chain A and (resid 1 through 57 or resid 59...A8 - 795
1121(chain A and (resid 1 through 57 or resid 59...A742 - 745
1131(chain A and (resid 1 through 57 or resid 59...A747 - 795
211(chain B and (resid 1 through 57 or resid 59...B1 - 57
221(chain B and (resid 1 through 57 or resid 59...B59 - 379
231(chain B and (resid 1 through 57 or resid 59...B381 - 386
241(chain B and (resid 1 through 57 or resid 59...B388 - 451
251(chain B and (resid 1 through 57 or resid 59...B453 - 468
261(chain B and (resid 1 through 57 or resid 59...B8 - 796
271(chain B and (resid 1 through 57 or resid 59...B545 - 597
281(chain B and (resid 1 through 57 or resid 59...B599 - 43
291(chain B and (resid 1 through 57 or resid 59...B645 - 694
2101(chain B and (resid 1 through 57 or resid 59...B696 - 714
2111(chain B and (resid 1 through 57 or resid 59...B722 - 7
2121(chain B and (resid 1 through 57 or resid 59...B742
2131(chain B and (resid 1 through 57 or resid 59...B747 - 795
311(chain C and (resid 1 through 2 or resid 8...C1 - 2
321(chain C and (resid 1 through 2 or resid 8...C8 - 57
331(chain C and (resid 1 through 2 or resid 8...C59 - 379
341(chain C and (resid 1 through 2 or resid 8...C381 - 386
351(chain C and (resid 1 through 2 or resid 8...C388 - 451
361(chain C and (resid 1 through 2 or resid 8...C453 - 468
371(chain C and (resid 1 through 2 or resid 8...C541 - 543
381(chain C and (resid 1 through 2 or resid 8...C545 - 597
391(chain C and (resid 1 through 2 or resid 8...C599 - 643
3101(chain C and (resid 1 through 2 or resid 8...C645 - 694
3111(chain C and (resid 1 through 2 or resid 8...C696 - 732
3121(chain C and (resid 1 through 2 or resid 8...C742 - 745
3131(chain C and (resid 1 through 2 or resid 8...C747 - 795
411(chain D and (resid 1 through 2 or resid 8...D1 - 2
421(chain D and (resid 1 through 2 or resid 8...D8 - 57
431(chain D and (resid 1 through 2 or resid 8...D59 - 379
441(chain D and (resid 1 through 2 or resid 8...D381 - 386
451(chain D and (resid 1 through 2 or resid 8...D388 - 451
461(chain D and (resid 1 through 2 or resid 8...D453 - 468
471(chain D and (resid 1 through 2 or resid 8...D541 - 543
481(chain D and (resid 1 through 2 or resid 8...D545 - 597
491(chain D and (resid 1 through 2 or resid 8...D599 - 643
4101(chain D and (resid 1 through 2 or resid 8...D645 - 694
4111(chain D and (resid 1 through 2 or resid 8...D696 - 714
4121(chain D and (resid 1 through 2 or resid 8...D722 - 732
4131(chain D and (resid 1 through 2 or resid 8...D742 - 745
4141(chain D and (resid 1 through 2 or resid 8...D747 - 795

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Maltodextrin-binding protein, Protein APCDD1 complex / Adenomatosis polyposis coli down-regulated 1 protein homolog


Mass: 91658.289 Da / Num. of mol.: 4
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)
Plasmid: pHLsec / Gene: Apcdd1, Drapc1 / Production host: Homo sapiens (human) / References: UniProt: C3SHQ8, UniProt: Q3U128

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Sugars , 2 types, 16 molecules

#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / 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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Non-polymers , 5 types, 656 molecules

#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-DMX / 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE


Mass: 257.349 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H19NO3S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M ammonium citrate, pH 7.0, 20% PEG3350, 4% NDSB-256, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→39.67 Å / Num. obs: 134251 / % possible obs: 90.5 % / Redundancy: 10.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.081 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.45 Å / Rmerge(I) obs: 5.124 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 6708 / CC1/2: 0.229 / Rpim(I) all: 1.749

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å39.6 Å
Translation2.5 Å39.6 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
xia2data reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SET

3set


Resolution: 2.33→39.67 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 1972 1.48 %
Rwork0.1924 131015 -
obs0.1932 132987 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.49 Å2 / Biso mean: 70 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: final / Resolution: 2.33→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24758 0 380 643 25781
Biso mean--75.73 51.83 -
Num. residues----3133
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9140X-RAY DIFFRACTION11.084TORSIONAL
12B9140X-RAY DIFFRACTION11.084TORSIONAL
13C9140X-RAY DIFFRACTION11.084TORSIONAL
14D9140X-RAY DIFFRACTION11.084TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.33-2.390.3472150.3383118311
2.39-2.450.3567540.3332453042
2.45-2.520.36161440.3117831778
2.52-2.60.34321510.31221036498
2.6-2.70.34221650.301110557100
2.7-2.810.3441640.279210612100
2.81-2.930.32681560.257110574100
2.93-3.090.3331530.243310627100
3.09-3.280.28041650.218810633100
3.28-3.530.24021540.186310634100
3.53-3.890.21631600.161910682100
3.89-4.450.19471640.140710714100
4.45-5.610.1631600.136510748100
5.61-39.670.20141670.17071084099
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)
11.12990.4003-0.042-0.10230.44840.5582-0.15930.42120.1350.02180.0862-0.16890.0814-0.2304-0.21280.3191-0.1626-0.01290.41880.0802-0.0015-22.1287-29.291724.2572
21.33350.0259-0.85660.46690.00370.84120.1069-0.02060.0958-0.0677-0.00920.0527-0.05740.06790.0010.2645-0.0066-0.00450.21170.02060.2847-8.2592-9.151557.51
30.5051-0.3469-0.02140.751-0.10830.71440.18080.22890.0327-0.7472-0.0713-0.0176-0.06340.45070.10190.8636-0.14720.2241.0304-0.09050.4179-27.789319.251315.8585
41.26930.4481-0.40520.3375-0.18470.7193-0.13110.2663-0.0275-0.00910.0872-0.1520.0119-0.0714-0.04840.2472-0.07550.08310.1826-0.02770.408-8.063136.329854.9002
50.9418-0.46970.19550.8287-0.14331.4149-0.0893-0.26420.10240.05410.0291-0.11090.175-0.2481-0.02240.44110.0084-0.0590.4464-0.04750.267827.3298-11.9851131.4677
60.3231-0.4949-0.00480.2533-0.18780.23190.0328-0.01010.1249-0.0287-0.0381-0.03320.18350.091700.40460.0621-0.0640.2948-0.0040.339828.7255-4.273110.9392
70.48740.30470.23220.1256-0.03450.4714-0.06410.06180.2181-0.0710.10370.3560.0824-0.2460.02160.28410.0372-0.03370.3277-0.04180.4406-2.989614.622790.8007
80.35650.30650.36450.41640.3020.50120.1232-0.07570.05650.0555-0.10630.04520.1874-0.01360.00010.25370.0327-0.05720.22670.00060.27637.2578.909194.5405
90.52040.0590.0160.59260.50950.25140.04870.02280.0272-0.01080.0445-0.2033-0.02950.05640.00390.2710.0403-0.03090.2276-0.01810.30429.842617.528295.4031
100.05810.04810.10020.08270.01660.07340.20890.1441-0.32410.0301-0.1563-0.45420.19620.0458-0.00020.36030.01860.04490.39160.04030.50154.7336-18.360725.9504
110.83110.01720.19630.90770.11950.80560.03220.15230.0676-0.2759-0.0487-0.0112-0.11760.035-0.00340.3784-0.02520.03120.30530.06510.233833.4604-10.575723.3152
120.7082-0.08790.33950.30810.20870.5203-0.04270.0576-0.1323-0.06020.1016-0.04560.04530.08970.00010.2683-0.0483-0.00390.2687-0.02240.27864.29911.951958.3434
130.32440.12310.01920.2112-0.10270.0774-0.110.1190.0405-0.07230.24940.11440.2231-0.02610.03910.2925-0.0994-0.02820.2814-0.02550.256657.445411.772752.6395
140.1460.12040.03150.0253-0.00010.06060.1641-0.20620.345-0.0295-0.17760.1542-0.06180.0339-00.3503-0.056-0.03180.42390.07360.415235.513216.222457.9428
150.1186-0.05960.23540.0346-0.13810.2183-0.2096-0.18860.34170.09690.20910.0169-0.4208-0.0585-0.00370.38170.09210.05050.46640.05260.490534.088222.36264.1207
160.43120.15850.01090.4004-0.33210.425-0.09470.00180.295-0.10510.17590.050.0685-0.00060.00620.3391-0.0739-0.03380.3431-0.02760.452843.411821.28854.8304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 437 )A8 - 437
2X-RAY DIFFRACTION2chain 'A' and (resid 438 through 795 )A438 - 795
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 336 )B8 - 336
4X-RAY DIFFRACTION4chain 'B' and (resid 337 through 796 )B337 - 796
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 317 )C6 - 317
6X-RAY DIFFRACTION6chain 'C' and (resid 318 through 415 )C318 - 415
7X-RAY DIFFRACTION7chain 'C' and (resid 416 through 512 )C416 - 512
8X-RAY DIFFRACTION8chain 'C' and (resid 513 through 633 )C513 - 633
9X-RAY DIFFRACTION9chain 'C' and (resid 634 through 799 )C634 - 799
10X-RAY DIFFRACTION10chain 'D' and (resid 5 through 45 )D5 - 45
11X-RAY DIFFRACTION11chain 'D' and (resid 46 through 369 )D46 - 369
12X-RAY DIFFRACTION12chain 'D' and (resid 370 through 565 )D370 - 565
13X-RAY DIFFRACTION13chain 'D' and (resid 566 through 633 )D566 - 633
14X-RAY DIFFRACTION14chain 'D' and (resid 634 through 674 )D634 - 674
15X-RAY DIFFRACTION15chain 'D' and (resid 675 through 727 )D675 - 727
16X-RAY DIFFRACTION16chain 'D' and (resid 728 through 797 )D728 - 797

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