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- PDB-1jlj: 1.6 Angstrom crystal structure of the human neuroreceptor anchori... -

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Basic information

Entry
Database: PDB / ID: 1jlj
Title1.6 Angstrom crystal structure of the human neuroreceptor anchoring and molybdenum cofactor biosynthesis protein gephyrin
Componentsgephyrin
KeywordsSTRUCTURAL PROTEIN / globular alpha/beta fold
Function / homology
Function and homology information


glycine receptor clustering / molybdopterin cofactor biosynthetic process / Molybdenum cofactor biosynthesis / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering ...glycine receptor clustering / molybdopterin cofactor biosynthetic process / Molybdenum cofactor biosynthesis / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / molybdopterin cofactor binding / response to metal ion / postsynaptic specialization, intracellular component / neurotransmitter receptor localization to postsynaptic specialization membrane / synapse assembly / synaptic membrane / establishment of protein localization / GABA-ergic synapse / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / dendritic spine / postsynaptic membrane / cytoskeleton / postsynaptic density / signaling receptor binding / dendrite / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Molybdenum cofactor biosynthesis proteins signature 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) / Molybdenum cofactor biosynthesis, conserved site ...Molybdenum cofactor biosynthesis proteins signature 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) / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Gephyrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchwarz, G. / Schrader, N. / Mendel, R.R. / Hecht, H.-J. / Schindelin, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of human gephyrin and plant Cnx1 G domains: comparative analysis and functional implications.
Authors: Schwarz, G. / Schrader, N. / Mendel, R.R. / Hecht, H.J. / Schindelin, H.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gephyrin
B: gephyrin
C: gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5055
Polymers62,4363
Non-polymers692
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-61 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.269, 66.008, 73.122
Angle α, β, γ (deg.)90.00, 93.27, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1243-

HOH

Detailscontent of the assymetric unit corresponds to the biological active form of the trimeric gephyrin G domain

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Components

#1: Protein gephyrin / PUTATIVE GLYCINE RECEPTOR-TUBULIN LINKER PROTEIN


Mass: 20812.020 Da / Num. of mol.: 3 / Fragment: residues 1-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GEPHYRIN / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9NQX3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium formate, ammonium, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 294K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
123 mg/mlprotein1drop
20.6-0.7 Msodium formate1reservoir
30.1 Macetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.1
SYNCHROTRONNSLS X26C21.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 6, 2000
ADSC QUANTUM 42CCDNov 27, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 71681 / Num. obs: 64743 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.116 / Net I/σ(I): 14.4
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.283 / % possible all: 46.3
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 46.3 % / Rmerge(I) obs: 0.283

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DI6

1di6


Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: REFMAC library
Details: Scaling details: Babinet's principle for scaling has been used. Bulk solvent correction based on constant value has been used. Parameters for mask calculation. VDW prob radii = 1.40, ION ...Details: Scaling details: Babinet's principle for scaling has been used. Bulk solvent correction based on constant value has been used. Parameters for mask calculation. VDW prob radii = 1.40, ION probe radii = 0.80, Shrinkage radii = 0.80
RfactorNum. reflection% reflectionSelection details
Rfree0.18279 2623 4.1 %RANDOM
Rwork0.14676 ---
all0.1418 64743 --
obs0.14816 62069 90.3 %-
Solvent computationSolvent model: bulk solvent correction
Displacement parametersBiso mean: 18.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20.26 Å2
2---0.36 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 1 773 4730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.022
X-RAY DIFFRACTIONp_angle_d1.3991.994
X-RAY DIFFRACTIONp_mcbond_it2.0031.5
X-RAY DIFFRACTIONp_mcangle_it3.2862
X-RAY DIFFRACTIONp_scbond_it4.8453
X-RAY DIFFRACTIONp_scangle_it8.1134.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_plane_restr0.005
X-RAY DIFFRACTIONp_chiral_restr0.085

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