[English] 日本語
Yorodumi
- PDB-3qum: Crystal structure of human prostate specific antigen (PSA) in Fab... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qum
TitleCrystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high affinity and a PCa selective antibody
Components
  • Fab 5D3D11 Heavy Chain
  • Fab 5D3D11 Light Chain
  • Fab 5D5A5 Heavy Chain
  • Fab 5D5A5 Light Chain
  • Prostate-specific antigen
KeywordsIMMUNE SYSTEM / kallikrein fold / Prostate-specific antigen / serine protease / negative regulation of angiogenesis / natural post-transductional modification / N-linked and O-linked glycosylation
Function / homology
Function and homology information


semenogelase / positive regulation of antibacterial peptide production / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / protein metabolic process / serine-type peptidase activity / negative regulation of angiogenesis / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endopeptidase activity ...semenogelase / positive regulation of antibacterial peptide production / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / protein metabolic process / serine-type peptidase activity / negative regulation of angiogenesis / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endopeptidase activity / serine-type endopeptidase activity / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thomsen-Friedenreich antigen / Prostate-specific antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsStura, E.A. / Muller, B.H. / Michel, S. / Ducancel, F.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of human prostate-specific antigen in a sandwich antibody complex.
Authors: Stura, E.A. / Muller, B.H. / Bossus, M. / Michel, S. / Jolivet-Reynaud, C. / Ducancel, F.
#1: Journal: J.Mol.Biol. / Year: 2011
Title: In Vitro Affinity Maturation of an Anti-PSA Antibody for Prostate Cancer Diagnostic Assay.
Authors: Muller, B.H. / Savatier, A. / L'hostis, G. / Costa, N. / Bossus, M. / Michel, S. / Ott, C. / Becquart, L. / Ruffion, A. / Stura, E.A. / Ducancel, F.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: Prostate-specific antigen
L: Fab 5D3D11 Light Chain
H: Fab 5D3D11 Heavy Chain
A: Fab 5D5A5 Light Chain
B: Fab 5D5A5 Heavy Chain
Q: Prostate-specific antigen
M: Fab 5D3D11 Light Chain
K: Fab 5D3D11 Heavy Chain
C: Fab 5D5A5 Light Chain
D: Fab 5D5A5 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,83813
Polymers243,40110
Non-polymers6,4373
Water1,63991
1
P: Prostate-specific antigen
L: Fab 5D3D11 Light Chain
H: Fab 5D3D11 Heavy Chain
A: Fab 5D5A5 Light Chain
B: Fab 5D5A5 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1117
Polymers121,7015
Non-polymers3,4102
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: Prostate-specific antigen
M: Fab 5D3D11 Light Chain
K: Fab 5D3D11 Heavy Chain
C: Fab 5D5A5 Light Chain
D: Fab 5D5A5 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7276
Polymers121,7015
Non-polymers3,0271
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.308, 226.883, 118.694
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 4 types, 8 molecules LMHKACBD

#2: Antibody Fab 5D3D11 Light Chain


Mass: 24271.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab 5D3D11 Heavy Chain


Mass: 23551.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody Fab 5D5A5 Light Chain


Mass: 24189.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody Fab 5D5A5 Heavy Chain


Mass: 23565.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Protein / Non-polymers , 2 types, 93 molecules PQ

#1: Protein Prostate-specific antigen / / PSA / Gamma-seminoprotein / Seminin / Kallikrein-3 / P-30 antigen / Semenogelase


Mass: 26122.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P07288, semenogelase
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 3 types, 3 molecules

#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 3026.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-4DManpa1-3[DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-2[DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,15,14/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-2-1-3-4-2-1-3-4-1-3-4-5/a4-b1_a6-o1_b4-c1_c3-d1_c6-h1_d4-e1_e4-f1_f3-g2_h2-i1_h6-l1_i4-j1_j3-k2_l4-m1_m3-n2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen / Thomsen–Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#8: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 3026.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-6DManpa1-3[DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-2[DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,15,14/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-2-1-3-4-2-1-3-4-1-3-4-5/a4-b1_a6-o1_b4-c1_c3-d1_c6-h1_d6-e1_e4-f1_f3-g2_h2-i1_h6-l1_i4-j1_j3-k2_l4-m1_m3-n2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: 20 ul 5D3D11 at 10.7 mg/ml and 10 ul PSA at 5 mg/ml + 31 ul 5D5A5 at 6.7mg/ml in PBS. against a precipitant of 10% PEG 4,000, 20% ethylene glycol, 100 mM Na,K phosphate. ...Details: Protein solution: 20 ul 5D3D11 at 10.7 mg/ml and 10 ul PSA at 5 mg/ml + 31 ul 5D5A5 at 6.7mg/ml in PBS. against a precipitant of 10% PEG 4,000, 20% ethylene glycol, 100 mM Na,K phosphate. Drops consisted of 1 ul protein + precipitant equilibrated by vapor diffusion. Streak seeding and macro seeding were used, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2007
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: diffracting Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→81.65 Å / Num. all: 47764 / Num. obs: 47573 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 83.924 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.2-3.372.40.7911.768640.5998.8
3.37-3.582.40.5032.865490.3799.3
3.58-3.822.40.3873.861520.27399.6
3.82-4.132.50.1986.257800.15599.9
4.13-4.532.50.09710.352940.08499.9
4.53-5.062.60.07312.848330.06799.9
5.06-5.842.60.06913.542000.0699.9
5.84-7.162.60.06514.735870.06199.8
7.16-10.122.60.06818.627740.07899.6
10.12-81.652.50.07120.415400.05799

-
Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZCH, using individual PSA and Fab as independent search models.

2zch


Resolution: 3.2→58.965 Å / SU ML: 0.48 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): -3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2937 2367 5.05 %RANDOM
Rwork0.1984 ---
obs0.2032 46916 98.18 %-
all-47764 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.872 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 73.269 Å2
Baniso -1Baniso -2Baniso -3
1-2.2654 Å20 Å2-1.5974 Å2
2---2.5605 Å2-0 Å2
3---0.2951 Å2
Refinement stepCycle: LAST / Resolution: 3.2→58.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17078 0 437 91 17606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117933
X-RAY DIFFRACTIONf_angle_d1.62324399
X-RAY DIFFRACTIONf_dihedral_angle_d22.4086507
X-RAY DIFFRACTIONf_chiral_restr0.1082764
X-RAY DIFFRACTIONf_plane_restr0.0083063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.26540.40591220.29982348X-RAY DIFFRACTION87
3.2654-3.33640.39531360.27692403X-RAY DIFFRACTION92
3.3364-3.4140.33661310.25122593X-RAY DIFFRACTION96
3.414-3.49940.32811330.23182649X-RAY DIFFRACTION99
3.4994-3.5940.35141540.2442643X-RAY DIFFRACTION100
3.594-3.69970.36431410.27452665X-RAY DIFFRACTION99
3.6997-3.81910.40681310.27692616X-RAY DIFFRACTION100
3.8191-3.95560.30611420.20762711X-RAY DIFFRACTION100
3.9556-4.11390.29731370.18262620X-RAY DIFFRACTION100
4.1139-4.30110.2471520.16422642X-RAY DIFFRACTION100
4.3011-4.52780.26331540.1432657X-RAY DIFFRACTION100
4.5278-4.81130.23351300.14322662X-RAY DIFFRACTION100
4.8113-5.18260.28021510.15432664X-RAY DIFFRACTION100
5.1826-5.70380.25721240.18252698X-RAY DIFFRACTION100
5.7038-6.52820.29261410.21322649X-RAY DIFFRACTION100
6.5282-8.22130.32281400.19142684X-RAY DIFFRACTION100
8.2213-58.97480.23661480.19112645X-RAY DIFFRACTION98

+
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