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- PDB-6rti: X-ray structure of human glutamate carboxypeptidase II (GCPII) in... -

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Basic information

Entry
Database: PDB / ID: 6rti
TitleX-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with aptamer A9g
Components
  • Aptamer A9g, RNA (43-MER)
  • Glutamate carboxypeptidase 2
KeywordsHYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / aptamer
Function / homology
Function and homology information


Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity ...Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity / cell surface / proteolysis / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A ...Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID / RNA / RNA (> 10) / Glutamate carboxypeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMotlova, L. / Kolenko, P. / Barinka, C.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer.
Authors: Ptacek, J. / Zhang, D. / Qiu, L. / Kruspe, S. / Motlova, L. / Kolenko, P. / Novakova, Z. / Shubham, S. / Havlinova, B. / Baranova, P. / Chen, S.J. / Zou, X. / Giangrande, P. / Barinka, C.
History
DepositionMay 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 23, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 24, 2024Group: 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
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: Glutamate carboxypeptidase 2
X: Aptamer A9g, RNA (43-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,36121
Polymers93,3792
Non-polymers4,98219
Water7,224401
1
A: Glutamate carboxypeptidase 2
X: Aptamer A9g, RNA (43-MER)
hetero molecules

A: Glutamate carboxypeptidase 2
X: Aptamer A9g, RNA (43-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,72242
Polymers186,7584
Non-polymers9,96438
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area25440 Å2
ΔGint-212 kcal/mol
Surface area60370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.096, 121.096, 216.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1099-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AX

#1: Protein Glutamate carboxypeptidase 2 / Cell growth-inhibiting gene 27 protein / Folate hydrolase 1 / Folylpoly-gamma-glutamate ...Cell growth-inhibiting gene 27 protein / Folate hydrolase 1 / Folylpoly-gamma-glutamate carboxypeptidase / FGCP / Glutamate carboxypeptidase II / GCPII / Membrane glutamate carboxypeptidase / mGCP / N-acetylated-alpha-linked acidic dipeptidase I / NAALADase I / Prostate-specific membrane antigen / PSMA / Pteroylpoly-gamma-glutamate carboxypeptidase


Mass: 79614.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneiders S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II
#2: RNA chain Aptamer A9g, RNA (43-MER)


Mass: 13764.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: All the pyrimidines were 2' fluoro modified. / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 7 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 413 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-G88 / (2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID


Mass: 226.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O7P
#10: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#11: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.25 Å3/Da / Density % sol: 71.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.2 Mg Acet, 40% (v/v) MPD, 1 mM 2-PMPA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→105.66 Å / Num. obs: 82266 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.838 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.048 / Rrim(I) all: 0.172 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
5.97-105.6611.90.04631.444990.7340.0160.05
2.2-2.2412.90.985240510.5780.2841.026

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OOT

2oot


Resolution: 2.2→105.66 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 5.163 / SU ML: 0.118 / Cross valid method: FREE R-VALUE / ESU R: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4036 5 %Random
Rwork0.192 82168 --
all0.195 ---
obs0.195 82168 99.989 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1-1.711 Å2-0 Å2-0 Å2
2--1.711 Å2-0 Å2
3----3.421 Å2
Refinement stepCycle: LAST / Resolution: 2.2→105.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5521 907 321 401 7150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137172
X-RAY DIFFRACTIONr_bond_other_d0.0070.0185937
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.7489904
X-RAY DIFFRACTIONr_angle_other_deg1.3741.73613871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27922.313307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20415948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3671533
X-RAY DIFFRACTIONr_chiral_restr0.0730.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021540
X-RAY DIFFRACTIONr_nbd_refined0.180.21334
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25816
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23298
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1080.22657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2445
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.222
X-RAY DIFFRACTIONr_nbd_other0.2090.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.213
X-RAY DIFFRACTIONr_mcbond_it2.3444.2862792
X-RAY DIFFRACTIONr_mcbond_other2.3444.2842789
X-RAY DIFFRACTIONr_mcangle_it3.4966.4263487
X-RAY DIFFRACTIONr_mcangle_other3.4966.4263488
X-RAY DIFFRACTIONr_scbond_it3.0625.0364378
X-RAY DIFFRACTIONr_scbond_other3.0625.0374379
X-RAY DIFFRACTIONr_scangle_it4.6327.4556412
X-RAY DIFFRACTIONr_scangle_other4.6317.4566413
X-RAY DIFFRACTIONr_lrange_it6.16851.7858245
X-RAY DIFFRACTIONr_lrange_other6.15151.668170
LS refinement shellResolution: 2.2→2.257 Å
RfactorNum. reflection% reflection
Rfree0.363 293 5 %
Rwork0.352 5690 -
obs--99.9499 %

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