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- PDB-4pd0: 1.7 A resolution structure of gephyrin's E-domain -

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Basic information

Entry
Database: PDB / ID: 4pd0
Title1.7 A resolution structure of gephyrin's E-domain
ComponentsGephyrin
KeywordsBiosynthetic Protein / Structural Protein / Scaffolding protein / Neurotransmitter receptor anchoring protein / Molybdenum cofactor biosynthesis
Function / homology
Function and homology information


Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / nitrate reductase activity / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / response to metal ion / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / GABA-ergic synapse / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynaptic membrane / postsynapse / postsynaptic density / molecular adaptor activity / cytoskeleton / signaling receptor binding / dendrite / neuronal cell body / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKasaragod, V.B. / Maric, H.M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schi 425/8-1 Germany
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Modulation of gephyrin-glycine receptor affinity by multivalency.
Authors: Maric, H.M. / Kasaragod, V.B. / Schindelin, H.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Dec 3, 2014Group: Database references
Revision 1.4Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _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
A: Gephyrin


Theoretical massNumber of molelcules
Total (without water)45,6521
Polymers45,6521
Non-polymers00
Water5,927329
1
A: Gephyrin

A: Gephyrin


Theoretical massNumber of molelcules
Total (without water)91,3052
Polymers91,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area6120 Å2
ΔGint-22 kcal/mol
Surface area36200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.655, 100.008, 113.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-824-

HOH

21A-934-

HOH

31A-936-

HOH

41A-1084-

HOH

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Components

#1: Protein Gephyrin / / Putative glycine receptor-tubulin linker protein


Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: E-domain (UNP residues 350-768)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium-citrate, pH 4.5, 28-34% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.7→43.83 Å / Num. obs: 55179 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FU3

2fu3


Resolution: 1.7→43.828 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 2800 5.08 %Random selection
Rwork0.1606 ---
obs0.1618 55170 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→43.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 0 329 3502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113264
X-RAY DIFFRACTIONf_angle_d1.3224448
X-RAY DIFFRACTIONf_dihedral_angle_d12.6261249
X-RAY DIFFRACTIONf_chiral_restr0.08520
X-RAY DIFFRACTIONf_plane_restr0.007588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72940.25991320.23412611X-RAY DIFFRACTION100
1.7294-1.76080.27231430.23082577X-RAY DIFFRACTION100
1.7608-1.79470.24521390.22582590X-RAY DIFFRACTION100
1.7947-1.83130.27131110.21772624X-RAY DIFFRACTION100
1.8313-1.87110.27221350.20672599X-RAY DIFFRACTION100
1.8711-1.91470.2541230.20032589X-RAY DIFFRACTION100
1.9147-1.96250.19911260.17892607X-RAY DIFFRACTION100
1.9625-2.01560.20261460.17832588X-RAY DIFFRACTION100
2.0156-2.07490.19031470.16482595X-RAY DIFFRACTION100
2.0749-2.14190.18071380.15632613X-RAY DIFFRACTION100
2.1419-2.21840.20011510.15962574X-RAY DIFFRACTION100
2.2184-2.30730.19311430.15382614X-RAY DIFFRACTION100
2.3073-2.41230.18591480.14312615X-RAY DIFFRACTION100
2.4123-2.53940.17811410.14892590X-RAY DIFFRACTION100
2.5394-2.69850.16731510.16252607X-RAY DIFFRACTION100
2.6985-2.90680.20871400.15932644X-RAY DIFFRACTION100
2.9068-3.19930.16271410.15712622X-RAY DIFFRACTION100
3.1993-3.6620.17241410.14852666X-RAY DIFFRACTION100
3.662-4.61290.14081500.13372675X-RAY DIFFRACTION100
4.6129-43.8420.19231540.17022770X-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)
11.8268-0.7019-1.27583.33553.16795.35160.06920.051-0.1482-0.25990.198-0.31270.03780.4257-0.23940.18790.0602-0.01970.1860.03190.196819.127130.7893107.6308
23.20891.2742-3.61850.5367-1.24434.12490.2052-0.297-0.06970.1401-0.19520.0465-0.17730.16380.00430.2463-0.04070.00930.29150.03040.2553-5.649130.4972153.9796
30.6068-0.00091.17190.4915-0.80267.3204-0.00980.1056-0.0133-0.0625-0.0165-0.0121-0.09630.02340.05320.1680.02010.01050.1880.00140.22946.688939.6064105.5499
43.4453-0.0547-0.32444.7959-0.66181.5075-0.03410.5790.1686-0.610.0188-0.2811-0.01080.3163-0.0040.22410.02340.02910.34580.02420.227520.083836.947794.253
52.06071.80060.09492.921-0.23841.3131-0.1030.1122-0.1454-0.24430.10160.08080.3266-0.0468-0.00830.2610.04-0.01350.1679-0.00790.23885.505719.6739104.0162
65.9233-3.0106-2.00615.02630.93182.74930.19011.26730.3651-0.8957-0.05571.16990.0296-0.6296-0.06740.3829-0.0281-0.11370.39420.06830.4881-6.202918.8355100.4723
73.97941.79412.06672.9751-1.41274.38780.07140.3437-0.6642-0.4022-0.0261-0.24940.64820.1625-0.0010.38220.03570.05790.1924-0.02980.37355.69469.649999.5824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 319 through 349 )
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 472 )
3X-RAY DIFFRACTION3chain 'A' and (resid 473 through 550 )
4X-RAY DIFFRACTION4chain 'A' and (resid 551 through 627 )
5X-RAY DIFFRACTION5chain 'A' and (resid 628 through 686 )
6X-RAY DIFFRACTION6chain 'A' and (resid 687 through 712 )
7X-RAY DIFFRACTION7chain 'A' and (resid 713 through 736 )

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