[English] 日本語
Yorodumi
- PDB-3qv1: Crystal structure of the binary complex of photosyntetic A4 glyce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qv1
TitleCrystal structure of the binary complex of photosyntetic A4 glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with cp12-2, both from Arabidopsis thaliana.
Components
  • CP12 protein
  • Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / Rossmann fold / Calvin cycle / NAD / 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 / DI(HYDROXYETHYL)ETHER / 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 Å
AuthorsThumiger, A. / Fermani, S. / 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. / Thumiger, A. / Pupillo, P. / Falini, G. / Trost, P.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.4Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: CP12 protein
H: CP12 protein
I: CP12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,16621
Polymers244,6139
Non-polymers4,55312
Water3,441191
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
G: CP12 protein
H: CP12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,30116
Polymers163,0756
Non-polymers3,22610
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25290 Å2
ΔGint-154 kcal/mol
Surface area43390 Å2
MethodPISA
2
E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
I: CP12 protein
hetero molecules

E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
I: CP12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,72910
Polymers163,0756
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area23040 Å2
ΔGint-133 kcal/mol
Surface area43980 Å2
MethodPISA
3
A: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
D: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
G: CP12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2699
Polymers81,5383
Non-polymers1,7316
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-69 kcal/mol
Surface area26630 Å2
MethodPISA
4
B: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
C: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
H: CP12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0337
Polymers81,5383
Non-polymers1,4954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-33 kcal/mol
Surface area26570 Å2
MethodPISA
5
E: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules

F: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
I: CP12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8645
Polymers81,5383
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation4_565x,-y+1,-z1
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-36 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.670, 245.990, 138.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 2 types, 9 molecules ABCDEFGHI

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


Mass: 36391.570 Da / Num. of mol.: 6 / Fragment: UNP residues 60-396
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 CP12 protein


Mass: 8754.368 Da / Num. of mol.: 3 / Fragment: UNP residues 54-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g62410, T12C14_110 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LZP9

-
Non-polymers , 5 types, 203 molecules

#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% (w/v) PEG 4K, 0.6 M NaCl, 1 mM NAD and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→34.2 Å / Num. all: 168053 / Num. obs: 163587 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.3 / Num. unique all: 24070 / Rsym value: 0.716 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2B

3k2b


Resolution: 2→34.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.434 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27243 8137 5 %RANDOM
Rwork0.22537 ---
all0.22776 153928 --
obs0.22776 153928 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.638 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20 Å20 Å2
2---0.67 Å20 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 2→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15827 0 299 191 16317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215096
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.98222373
X-RAY DIFFRACTIONr_angle_other_deg0.824335152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09452077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57824.636660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.292152770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5991593
X-RAY DIFFRACTIONr_chiral_restr0.0950.22621
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023051
X-RAY DIFFRACTIONr_nbd_refined0.2140.33433
X-RAY DIFFRACTIONr_nbd_other0.2260.315865
X-RAY DIFFRACTIONr_nbtor_refined0.1850.57788
X-RAY DIFFRACTIONr_nbtor_other0.0970.59183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.51031
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0650.58
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.344
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.3198
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.527
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0640.51
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.47213115
X-RAY DIFFRACTIONr_mcbond_other0.2824256
X-RAY DIFFRACTIONr_mcangle_it1.801316713
X-RAY DIFFRACTIONr_scbond_it1.10727006
X-RAY DIFFRACTIONr_scangle_it1.59535656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 600 -
Rwork0.329 11349 -
obs--99.31 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more