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- PDB-6zr7: X-ray structure of human Dscam Ig7-Ig9 -

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Basic information

Entry
Database: PDB / ID: 6zr7
TitleX-ray structure of human Dscam Ig7-Ig9
ComponentsDown syndrome cell adhesion molecule
KeywordsCELL ADHESION / neuronal self-avoidance / N-glycosylation
Function / homology
Function and homology information


post-embryonic retina morphogenesis in camera-type eye / camera-type eye photoreceptor cell differentiation / netrin receptor binding / retina layer formation / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of axon extension involved in axon guidance / negative regulation of cell adhesion / dendrite morphogenesis / DSCAM interactions ...post-embryonic retina morphogenesis in camera-type eye / camera-type eye photoreceptor cell differentiation / netrin receptor binding / retina layer formation / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of axon extension involved in axon guidance / negative regulation of cell adhesion / dendrite morphogenesis / DSCAM interactions / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / positive regulation of phosphorylation / synapse assembly / protein tyrosine kinase binding / locomotory behavior / axon guidance / nervous system development / growth cone / cell adhesion / axon / neuronal cell body / synapse / dendrite / extracellular region / membrane / plasma membrane
Similarity search - Function
Cell adhesion molecule DSCAM, metazoan / Basigin-like / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type ...Cell adhesion molecule DSCAM, metazoan / Basigin-like / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / Down syndrome cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKozak, S. / Bento, I. / Meijers, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis.
Authors: Kozak, S. / Bloch, Y. / De Munck, S. / Mikula, A. / Bento, I. / Savvides, S.N. / Meijers, R.
History
DepositionJul 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Down syndrome cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0497
Polymers34,2541
Non-polymers1,7956
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, size-exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint15 kcal/mol
Surface area17420 Å2
Unit cell
Length a, b, c (Å)78.599, 71.421, 92.174
Angle α, β, γ (deg.)90.000, 113.061, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Down syndrome cell adhesion molecule / CHD2


Mass: 34254.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSCAM / Production host: Homo sapiens (human) / References: UniProt: O60469

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Sugars , 3 types, 4 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#6: 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.: 1
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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Non-polymers , 3 types, 168 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.48 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5 / Details: Glycerol, calcium acetate, PEG 8000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationMonochromator: Double Crystal Monochromator FMB Oxford / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→84.81 Å / Num. obs: 39662 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.026 / Rrim(I) all: 0.051 / Net I/σ(I): 12.8
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.874 / Num. unique obs: 2418 / CC1/2: 0.7 / Rpim(I) all: 0.501 / Rrim(I) all: 1.011 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wvr

4wvr


Resolution: 1.85→84.808 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.217 / SU B: 3.016 / SU ML: 0.088 / Average fsc free: 0.8942 / Average fsc work: 0.9078 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.228 2001 5.046 %
Rwork0.1947 37658 -
all0.196 --
obs-39659 98.782 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 56.811 Å2
Baniso -1Baniso -2Baniso -3
1--1.329 Å20 Å21.17 Å2
2--0.428 Å20 Å2
3----0.069 Å2
Refinement stepCycle: LAST / Resolution: 1.85→84.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 116 166 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132461
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182278
X-RAY DIFFRACTIONr_angle_refined_deg1.851.6873351
X-RAY DIFFRACTIONr_angle_other_deg1.3211.6075313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.645294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11722.793111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84615396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3531513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
X-RAY DIFFRACTIONr_nbd_refined0.1930.2340
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22072
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21124
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2147
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.215
X-RAY DIFFRACTIONr_nbd_other0.2070.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0420.23
X-RAY DIFFRACTIONr_mcbond_it5.4825.6431174
X-RAY DIFFRACTIONr_mcbond_other5.4835.6411173
X-RAY DIFFRACTIONr_mcangle_it7.2198.4371467
X-RAY DIFFRACTIONr_mcangle_other7.2178.441468
X-RAY DIFFRACTIONr_scbond_it6.8446.4081287
X-RAY DIFFRACTIONr_scbond_other6.8416.411288
X-RAY DIFFRACTIONr_scangle_it9.8679.3431883
X-RAY DIFFRACTIONr_scangle_other9.8659.3441884
X-RAY DIFFRACTIONr_lrange_it11.966.2912458
X-RAY DIFFRACTIONr_lrange_other11.89866.3122459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.3351530.30727530.30929810.7430.75497.48410.292
1.898-1.950.2941350.27926670.2828440.8170.83298.52320.26
1.95-2.0070.2711560.2625940.26127920.8540.86798.49570.24
2.007-2.0680.2671430.23825320.2427110.8760.88898.67210.219
2.068-2.1360.2541380.2224730.22226430.9050.91998.78930.202
2.136-2.2110.2521500.20823980.21125790.9190.92798.7980.19
2.211-2.2940.2291070.18923250.19124540.9310.94499.10350.174
2.294-2.3880.175990.19222360.19223550.9460.94199.15070.179
2.388-2.4940.2491260.2121380.21322830.9120.92399.16780.199
2.494-2.6160.271080.20620500.2121770.9170.93199.12720.197
2.616-2.7570.2681190.20719250.21120630.910.92999.0790.206
2.757-2.9240.254910.21618690.21819860.9150.92798.69080.218
2.924-3.1260.263880.19817500.20118490.9150.9499.40510.205
3.126-3.3760.246700.21716140.21817090.9160.92598.53720.229
3.376-3.6970.242940.19914900.20215970.9220.9499.1860.219
3.697-4.1330.201650.16913660.1714410.9460.95899.3060.193
4.133-4.770.144470.13312110.13412720.9760.97798.89940.161
4.77-5.8380.169510.14710160.14810770.970.97699.07150.18
5.838-8.2360.258390.1977970.28470.9430.9598.70130.238
8.236-84.8080.208220.2584540.2564880.9320.92997.5410.635

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