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- PDB-3rvd: Crystal structure of the binary complex, obtained by soaking, of ... -

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Basic information

Entry
Database: PDB / ID: 3rvd
TitleCrystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.
Components
  • Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
  • Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / Rossmann fold / Calvin cycle / binary complex / chloroplast / OXIDOREDUCTASE-PROTEIN BINDING complex
Function / homology
Function and homology information


peptide cross-linking via L-cystine / supramolecular complex / negative regulation of reductive pentose-phosphate cycle / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / response to sucrose ...peptide cross-linking via L-cystine / supramolecular complex / negative regulation of reductive pentose-phosphate cycle / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / response to sucrose / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast stroma / cellular response to cold / chloroplast thylakoid membrane / nickel cation binding / response to light stimulus / response to cold / chloroplast / glucose metabolic process / NAD binding / disordered domain specific binding / NADP binding / cellular response to heat / protein-containing complex assembly / protein-macromolecule adaptor activity / protein homotetramerization / copper ion binding / mRNA binding / protein-containing complex binding / enzyme binding / protein homodimerization activity / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain ...Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic / Calvin cycle protein CP12-2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFermani, S. / Thumiger, A. / Falini, G. / Marri, L. / Sparla, F. / Trost, P.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Conformational Selection and Folding-upon-binding of Intrinsically Disordered Protein CP12 Regulate Photosynthetic Enzymes Assembly.
Authors: Fermani, S. / Trivelli, X. / Sparla, F. / Thumiger, A. / Calvaresi, M. / Marri, L. / Falini, G. / Zerbetto, F. / Trost, P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform a4) from arabidopsis thaliana in complex with nad.
Authors: Fermani, S. / Sparla, F. / Marri, L. / Tumigher, A. / Pupillo, P. / Falini, G. / Trost, P.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 13, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
B: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
C: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
D: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
G: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
H: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
I: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
J: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
K: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
L: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
M: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
N: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Q: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,76654
Polymers416,44216
Non-polymers9,32438
Water10,016556
1
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
B: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
C: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
D: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
I: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
J: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,17025
Polymers163,0756
Non-polymers4,09519
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26120 Å2
ΔGint-330 kcal/mol
Surface area43760 Å2
2
E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
G: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
H: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
M: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
N: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,40117
Polymers163,0756
Non-polymers3,32611
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24570 Å2
ΔGint-259 kcal/mol
Surface area43700 Å2
3
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Q: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules

K: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
L: Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Q: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,88122
Polymers163,0756
Non-polymers3,80616
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_665-x+1,-y+1,z1
identity operation1_555x,y,z1
Buried area30160 Å2
ΔGint-390 kcal/mol
Surface area43460 Å2
Unit cell
Length a, b, c (Å)153.183, 188.750, 312.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-552-

HOH

21K-119-

HOH

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 36391.570 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g26650, GAPA, MLJ15.4, MLJ15_5 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P25856, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Protein
Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)


Mass: 8754.368 Da / Num. of mol.: 6 / Fragment: UNP residues 54-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g26650 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LZP9
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.4 M ammonium sulphate, 0.1 M sodium citrate, 1 mM NAD, 3.125 mg/ml CP12 for soaking experiments, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→95.3 Å / Num. all: 119322 / Num. obs: 118509 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 16.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.587 / % possible all: 84

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K2B

3k2b


Resolution: 2.7→94.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3188319.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.318 11850 10 %RANDOM
Rwork0.247 ---
obs0.247 118509 95.7 %-
all-119322 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.8944 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-31.48 Å20 Å20 Å2
2---11.8 Å20 Å2
3----19.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.7→94.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26538 0 580 556 27674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.372.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 1747 10 %
Rwork0.358 15758 -
obs--85.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6nad.paramnad.top

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