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- PDB-7jgz: Protocadherin gammaC4 EC1-4 crystal structure -

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Basic information

Entry
Database: PDB / ID: 7jgz
TitleProtocadherin gammaC4 EC1-4 crystal structure
ComponentsProtocadherin gamma C4
KeywordsCELL ADHESION / Protocadherin / Cadherin / Cell-surface receptor / Neuronal self-avoidance
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / synapse organization / negative regulation of neuron apoptotic process / membrane => GO:0016020 / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, N-terminal / Cadherin-like / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin gamma C4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Honig, B. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH114817 United States
CitationJournal: Elife / Year: 2022
Title: How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition.
Authors: Goodman, K.M. / Katsamba, P.S. / Rubinstein, R. / Ahlsen, G. / Bahna, F. / Mannepalli, S. / Dan, H. / Sampogna, R.V. / Shapiro, L. / Honig, B.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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: Protocadherin gamma C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,09315
Polymers47,0071
Non-polymers2,08614
Water00
1
A: Protocadherin gamma C4
hetero molecules

A: Protocadherin gamma C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,18630
Polymers94,0142
Non-polymers4,17328
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area8760 Å2
ΔGint-31 kcal/mol
Surface area43550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.220, 115.680, 194.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protocadherin gamma C4 / Protocadherin gamma subfamily C / 4


Mass: 47006.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgc4 / Cell line (production host): Freestyle 293-F cells / Production host: Homo sapiens (human) / References: UniProt: Q91XX0

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 10 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6O2

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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: 4.5 Å3/Da / Density % sol: 72.67 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 10% (w/v) PEG8000, 20% ethylene glycol, 10% Morpheus Amino Acids (Molecular Dimensions), and 0.1 M Morpheus Buffer System 2 (Hepes/MOPS buffer) pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 7545 / % possible obs: 67.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 77.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.086 / Rrim(I) all: 0.232 / Net I/σ(I): 8.3
Reflection shellResolution: 3.5→3.84 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 340 / CC1/2: 0.829 / Rpim(I) all: 0.335 / Rrim(I) all: 0.896 / % possible all: 12.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPO

4zpo


Resolution: 3.51→38.5 Å / SU ML: 0.4166 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.8692 / Stereochemistry target values: GeoStd + Monomer Library
Details: Please note ellipsoidal resolution limits of 4.6/3.9/3.5 were applied to the data. The completeness within the ellipsoidal limits is 96.8%.
RfactorNum. reflection% reflection
Rfree0.271 377 5 %
Rwork0.2234 7168 -
obs0.2257 7545 68.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.24 Å2
Refinement stepCycle: LAST / Resolution: 3.51→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 122 0 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393306
X-RAY DIFFRACTIONf_angle_d0.88894529
X-RAY DIFFRACTIONf_chiral_restr0.0499546
X-RAY DIFFRACTIONf_plane_restr0.0056598
X-RAY DIFFRACTIONf_dihedral_angle_d10.61061942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-4.010.2919370.3027694X-RAY DIFFRACTION20.37
4.01-5.050.29661510.24312874X-RAY DIFFRACTION83.4
5.05-38.50.25281890.20263600X-RAY DIFFRACTION100
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)
11.5735363577-0.1465561873231.97444704541.078244904310.5769663959233.02060876075-0.0880075353988-0.776400847203-0.3739630317610.463089060625-0.0418576163189-0.357910644913-1.012275555811.706503735790.02011263504891.15201958423-0.474792044901-0.3203752971441.88203025840.3563443999871.0616860683818.7202630825131.42474518656.163349786
23.35493322390.422433464590.3099176217232.62475272376-0.8598565942824.508444442160.16877634921-0.433359487772-0.6603950687870.0253288799882-0.270975645179-0.173890062413-0.2530324543340.1008391833240.07930833676360.754208576539-0.0905205303533-0.09104802865240.2230925013120.1599138836280.5590051350160.82854105661135.52727684316.7793676639
32.27284446515-0.1545931166830.8367407145272.10309675725-0.7547529409575.42734171416-0.1388861704860.25402574058-0.1829854221190.1652482895020.1869892179010.07605943302050.287748706578-0.3172137164580.04358272309950.5416087306810.112433691404-0.01282721016290.296753780786-0.1922341837560.440214082315-21.9971861672125.854175156-27.6935620566
43.501291825520.7182151100153.023148383761.267765750470.0913911151197.181493530.2622354388490.827142171227-0.298828470186-0.824820464298-0.2202638101390.386444625163-1.0064252114-0.837367165169-0.02618161815070.9687721655930.45505102834-0.05750120181291.32125922352-0.2285076258440.666265857946-39.4264651627122.163380819-72.494008894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 314 )
4X-RAY DIFFRACTION4chain 'A' and (resid 315 through 417 )

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