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- PDB-5k6z: Sidekick chimera containing sidekick-2 immunoglobulin domains 1-2... -

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Basic information

Entry
Database: PDB / ID: 5k6z
TitleSidekick chimera containing sidekick-2 immunoglobulin domains 1-2 and sidekick-1 immunoglobulin domains 3-4
ComponentsProtein sidekick-2,Protein sidekick-1 chimera
KeywordsCELL ADHESION / immunoglobulin
Function / homology
Function and homology information


SDK interactions / camera-type eye photoreceptor cell differentiation / retina layer formation / regulation of dendritic spine development / homophilic cell adhesion via plasma membrane adhesion molecules / behavioral response to cocaine / synapse assembly / synapse / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Protein sidekick-1 / Protein sidekick-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Honig, B. / Shapiro, L.
CitationJournal: Elife / Year: 2016
Title: Molecular basis of sidekick-mediated cell-cell adhesion and specificity.
Authors: Goodman, K.M. / Yamagata, M. / Jin, X. / Mannepalli, S. / Katsamba, P.S. / Ahlsen, G. / Sergeeva, A.P. / Honig, B. / Sanes, J.R. / Shapiro, L.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein sidekick-2,Protein sidekick-1 chimera
B: Protein sidekick-2,Protein sidekick-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7198
Polymers85,4792
Non-polymers1,2406
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-11 kcal/mol
Surface area36460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.350, 85.730, 146.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein sidekick-2,Protein sidekick-1 chimera


Mass: 42739.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sdk2, Kiaa1514, Sdk1 / Production host: Homo sapiens (human) / References: UniProt: Q6V4S5, UniProt: Q3UH53

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Sugars , 2 types, 3 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 40 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 6.9
Details: 3% (w/v) PEG8000, 40% (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. obs: 27743 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.99 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.7→45.374 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2329 1393 5.02 %
Rwork0.1928 --
obs0.1948 27742 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→45.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 77 37 5960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046075
X-RAY DIFFRACTIONf_angle_d0.7158292
X-RAY DIFFRACTIONf_dihedral_angle_d13.9783666
X-RAY DIFFRACTIONf_chiral_restr0.047942
X-RAY DIFFRACTIONf_plane_restr0.0041079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.79650.32021480.2682543X-RAY DIFFRACTION100
2.7965-2.90850.33181360.25522622X-RAY DIFFRACTION100
2.9085-3.04080.29771360.24332586X-RAY DIFFRACTION100
3.0408-3.20110.34751310.2292612X-RAY DIFFRACTION100
3.2011-3.40160.23931390.21072622X-RAY DIFFRACTION100
3.4016-3.66410.22731350.19112608X-RAY DIFFRACTION100
3.6641-4.03270.21951370.16462634X-RAY DIFFRACTION100
4.0327-4.61570.18161440.14372643X-RAY DIFFRACTION100
4.6157-5.81340.16461380.16042688X-RAY DIFFRACTION100
5.8134-45.38050.21011490.19562791X-RAY DIFFRACTION99
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)
10.82270.12431.31271.9965-1.49585.0898-0.12920.1658-0.0075-0.71380.25180.13680.2132-0.0399-0.12910.4309-0.0715-0.02740.2015-0.01930.197323.1495-0.058317.0376
21.65820.66152.282.1367-0.26736.64470.0520.008-0.1156-0.07280.13540.04360.0243-0.0375-0.17560.08930.00220.02190.20320.00920.171221.5462-0.61749.6457
34.9131-0.85982.871.7267-0.96324.197-0.17630.0775-0.0220.0862-0.0311-0.17830.10470.15380.19980.16510.02350.03160.11150.00080.200145.4001-8.18651.3809
43.2481-2.68221.99512.8082-2.46762.34660.22270.0343-0.4742-0.3820.13320.59860.2841-0.3734-0.29460.307-0.0256-0.16710.31170.01370.3695-1.304811.501416.4803
53.3248-0.21322.02974.0437-1.017.7060.06690.33220.6130.12450.03270.0656-0.29960.2263-0.10560.1723-0.01050.04660.26590.06610.343249.929513.490949.4914
62.8040.1236-0.8083.51580.16852.85680.0808-0.1212-0.04010.35680.1612-0.33050.02620.2631-0.23950.17950.0544-0.04690.3567-0.05170.27945.553932.402223.2727
72.46810.88890.7862.0298-0.25412.15730.02180.2588-0.0182-0.57390.1452-0.07380.40090.1101-0.15950.5044-0.04270.03950.1784-0.03230.221733.868615.8865.1264
82.3735-0.48290.0293.6607-1.14437.3465-0.10280.0090.2207-0.0126-0.0915-0.0252-0.4988-0.14510.18650.1328-0.0009-0.05010.1729-0.03110.222524.254617.384162.7739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 2:90))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 2:90))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 91:185))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 91:186))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 191:285))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 191:285))
7X-RAY DIFFRACTION7chain 'A' and ((resseq 286:379))
8X-RAY DIFFRACTION8chain 'B' and ((resseq 286:379))

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