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- PDB-5c7l: Structure of human testis-specific glyceraldehyde-3-phosphate deh... -

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Basic information

Entry
Database: PDB / ID: 5c7l
TitleStructure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase apo form
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, testis-specificGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / human sperm GAPDH metabolic enzyme sperm specific
Function / homology
Function and homology information


flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of glycolytic process / glycolytic process / glucose metabolic process / NAD binding ...flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of glycolytic process / glycolytic process / glucose metabolic process / NAD binding / NADP binding / nucleus / cytosol
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.862 Å
AuthorsBetts, L. / Machius, M. / Danshina, P. / O'Brien, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Mol. Hum. Reprod. / Year: 2016
Title: Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme.
Authors: Danshina, P.V. / Qu, W. / Temple, B.R. / Rojas, R.J. / Miley, M.J. / Machius, M. / Betts, L. / O'Brien, D.A.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
R: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific


Theoretical massNumber of molelcules
Total (without water)73,4782
Polymers73,4782
Non-polymers00
Water6,918384
1
O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
R: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific

O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
R: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific


Theoretical massNumber of molelcules
Total (without water)146,9554
Polymers146,9554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area15550 Å2
ΔGint-83 kcal/mol
Surface area44700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.888, 86.888, 159.606
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11O-601-

HOH

21R-539-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase, testis-specific / Glyceraldehyde 3-phosphate dehydrogenase / Spermatogenic cell-specific glyceraldehyde 3-phosphate dehydrogenase 2 / GAPDH-2 / Spermatogenic ...Spermatogenic cell-specific glyceraldehyde 3-phosphate dehydrogenase 2 / GAPDH-2 / Spermatogenic glyceraldehyde-3-phosphate dehydrogenase


Mass: 36738.758 Da / Num. of mol.: 2 / Fragment: unp residues 74-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDHS, GAPD2, GAPDH2, GAPDS, HSD-35, HSD35 / Production host: Escherichia coli (E. coli)
References: UniProt: O14556, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6.5
Details: mix 1:1 volume of protein at 10 mg/mL with 0.2 M sodium sulfate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0746 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0746 Å / Relative weight: 1
ReflectionResolution: 1.86→38.2 Å / Num. obs: 59104 / % possible obs: 99.8 % / Redundancy: 8.7 % / Net I/σ(I): 17.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 1.862→38.156 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1996 3.67 %
Rwork0.1865 52425 -
obs0.188 54421 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.51 Å2 / Biso mean: 32.7496 Å2 / Biso min: 8.76 Å2
Refinement stepCycle: final / Resolution: 1.862→38.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 0 384 5526
Biso mean---33.91 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135340
X-RAY DIFFRACTIONf_angle_d1.3997274
X-RAY DIFFRACTIONf_chiral_restr0.059814
X-RAY DIFFRACTIONf_plane_restr0.008946
X-RAY DIFFRACTIONf_dihedral_angle_d13.6941962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8619-1.90840.2597840.22062250233456
1.9084-1.960.28961090.22842736284568
1.96-2.01770.27271250.2373161328679
2.0177-2.08280.30161400.23143562370290
2.0828-2.15730.30451490.23493897404697
2.1573-2.24360.28521540.217440434197100
2.2436-2.34570.25411500.207940374187100
2.3457-2.46940.26981500.200640364186100
2.4694-2.6240.22061550.192640404195100
2.624-2.82660.21951570.191340654222100
2.8266-3.11090.22231550.18640874242100
3.1109-3.56080.22711530.17840964249100
3.5608-4.48510.17871540.156841284282100
4.4851-38.16430.19761610.16324287444899

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