[English] 日本語
Yorodumi
- PDB-6j15: Complex structure of GY-5 Fab and PD-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j15
TitleComplex structure of GY-5 Fab and PD-1
Components
  • GY-5 heavy chain Fab
  • GY-5 light chain Fab
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / Tumor immunotherapy / complex structure / FG loop
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, D. / Tan, S. / Zhang, H. / Wang, H. / Chai, Y. / Qi, J. / Yan, J. / Gao, G.F.
CitationJournal: Iscience / Year: 2019
Title: The FG Loop of PD-1 Serves as a "Hotspot" for Therapeutic Monoclonal Antibodies in Tumor Immune Checkpoint Therapy.
Authors: Chen, D. / Tan, S. / Zhang, H. / Wang, H. / He, W. / Shi, R. / Tong, Z. / Zhu, J. / Cheng, H. / Gao, S. / Chai, Y. / Qi, J. / Xiao, M. / Yan, J. / Gao, G.F.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: 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 / 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 / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Programmed cell death protein 1
D: Programmed cell death protein 1
H: GY-5 heavy chain Fab
L: GY-5 light chain Fab
A: GY-5 heavy chain Fab
B: GY-5 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,29610
Polymers122,5506
Non-polymers1,7464
Water00
1
C: Programmed cell death protein 1
A: GY-5 heavy chain Fab
B: GY-5 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2886
Polymers61,2753
Non-polymers1,0133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Programmed cell death protein 1
H: GY-5 heavy chain Fab
L: GY-5 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0084
Polymers61,2753
Non-polymers7331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.595, 64.347, 151.481
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules CD

#1: Protein Programmed cell death protein 1 / PD-1 / hPD-1


Mass: 13487.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q15116

-
Antibody , 2 types, 4 molecules HALB

#2: Antibody GY-5 heavy chain Fab


Mass: 23941.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody GY-5 light chain Fab


Mass: 23846.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Sugars , 3 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.1 M citrate (pH 5.0), 20% w/v polyethylene glycol 6000, 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33831 / % possible obs: 92.2 % / Redundancy: 6.2 % / Net I/σ(I): 3.17
Reflection shellResolution: 2.6→2.69 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ, 3EYQ

3rrq

3eyq


Resolution: 2.6→41.624 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2767 1698 5.02 %
Rwork0.2116 --
obs0.2148 33831 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 0 0 8342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018560
X-RAY DIFFRACTIONf_angle_d1.24811660
X-RAY DIFFRACTIONf_dihedral_angle_d19.983121
X-RAY DIFFRACTIONf_chiral_restr0.071329
X-RAY DIFFRACTIONf_plane_restr0.0071465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5955-2.67180.3673920.27291655X-RAY DIFFRACTION57
2.6718-2.7580.31811340.25752057X-RAY DIFFRACTION73
2.758-2.85660.33831160.27122434X-RAY DIFFRACTION84
2.8566-2.97090.351430.27212787X-RAY DIFFRACTION96
2.9709-3.10610.36361370.26822873X-RAY DIFFRACTION99
3.1061-3.26980.31151420.24642865X-RAY DIFFRACTION99
3.2698-3.47460.35851520.23042868X-RAY DIFFRACTION99
3.4746-3.74270.27681480.20952891X-RAY DIFFRACTION100
3.7427-4.1190.26771520.19442891X-RAY DIFFRACTION100
4.119-4.71430.22911510.15612918X-RAY DIFFRACTION100
4.7143-5.93680.22981530.16892923X-RAY DIFFRACTION100
5.9368-41.62940.22171780.21342971X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18570.30530.61851.87110.98292.0863-0.0859-0.5069-0.2664-0.30410.1859-0.0457-0.51390.1062-0.16560.1104-0.13910.05280.42370.03460.326259.54212.601241.1234
27.40463.0816-3.50414.4827-1.12634.40050.0967-0.3516-0.3935-0.41450.1610.3562-0.2948-0.9033-0.17250.18160.0372-0.12130.4450.01560.281437.34814.265133.0474
33.86320.90131.83680.98110.67983.91470.0945-0.0009-0.2149-0.04060.02830.0189-0.43380.0103-0.10840.1738-0.05620.07160.2042-0.01220.218951.276413.204848.1166
40.93430.073-0.31542.1429-2.8284.4275-0.5038-0.41740.51950.0883-0.0966-0.0312-1.1073-0.19380.52990.51-0.0136-0.15180.358-0.21140.524945.894322.857248.7082
53.2417-2.23972.61481.8083-1.61382.18780.3333-1.1651-0.79770.4610.59540.89250.0806-1.0228-0.23840.23530.01310.09640.57880.22810.426540.567210.542449.6284
61.26121.51640.88593.14730.44346.50440.160.05140.03420.01150.2267-0.0432-0.2072-0.227-0.32240.1603-0.04030.06780.2934-0.03520.267744.71813.256443.2873
75.31651.40190.95422.7212-0.24675.0923-0.17321.01670.12080.3080.28230.7959-1.06280.87480.23030.33-0.17820.01720.32540.04240.337759.176418.006150.5911
86.2143.8996-1.39195.95080.99691.9632-0.30420.45381.2144-0.9798-0.02860.6084-0.536-1.4903-0.24840.17690.11950.00290.5274-0.02650.274737.906419.368731.6631
93.36820.06922.74540.35890.2622.34670.05320.35830.5187-0.3104-0.54470.2526-0.00740.56440.05780.20450.054-0.01790.4523-0.03420.377854.217812.752630.576
105.4003-0.5781-0.85143.62160.4640.26940.30440.4947-0.20570.2061-0.3433-0.3230.57780.9232-0.04980.30550.120.01970.6876-0.01150.344874.40669.377336.0061
112.12410.26972.09920.4681-0.46192.9301-0.0411.4566-0.2804-0.03060.2888-0.3674-0.46041.66390.01410.18510.03990.02970.65450.09780.397765.667213.385521.5267
123.66762.77782.26756.13760.93451.55460.5835-0.3243-0.3717-0.9079-0.2913-1.50060.04791.4375-0.25120.3710.22980.07891.1832-0.0840.551675.02097.67123.2683
136.0359-0.94581.16832.3434-1.413.86280.3030.57270.1805-0.2225-0.3481-0.57410.69541.4039-0.16220.10960.07840.08411.1130.03550.546673.24538.538329.9316
142.50831.28172.45336.04281.76663.41690.6663-0.0026-0.04470.5187-0.1816-1.4664-0.37511.20910.02510.3847-0.1054-0.00070.58910.08420.410766.323316.946926.1767
152.709-1.90311.61031.4836-0.07929.9186-0.75-0.3040.10780.17340.0037-0.3415-0.65551.37760.37020.18360.01540.0230.3627-0.01190.337457.681818.051621.7109
166.0736-6.06232.77346.0636-3.11155.07630.566-0.87220.88730.5136-0.5489-0.6586-0.18920.5922-0.02950.1223-0.20080.03921.00450.03610.537278.738314.717240.6534
175.59810.89261.40928.69131.05186.2957-0.07740.3238-0.0905-1.21290.3972-0.8271-0.98451.1634-0.15580.3490.01520.15240.4463-0.01420.251654.076514.4422-14.0309
184.3011-0.4846-0.81094.1653-0.51664.80790.0520.0877-0.0618-0.3777-0.1087-0.26950.14390.76750.0260.26380.050.07370.2771-0.04160.180954.826214.2074-0.095
193.4631-2.26360.45854.46632.8777.25620.18540.2432-0.4079-1.00920.1625-0.1825-0.80750.4241-0.08540.2398-0.02570.1180.19680.05010.235549.580613.5591-5.1617
200.1393-0.54720.59730.308-0.79472.93730.17980.0542-0.0126-0.1423-0.05270.09240.23070.1436-0.13170.26730.01480.0010.11420.00140.240836.415220.43-20.3619
213.2842-2.62291.92092.052-1.63842.9982-0.00910.61670.9339-0.5109-0.2337-0.3099-0.1774-0.01140.10510.3879-0.014-0.02370.2028-0.01310.266529.837725.898-36.3824
227.7276-5.78985.25244.6236-4.41495.1430.2455-0.3586-0.6079-0.53950.22490.7541-0.0773-0.4271-0.35930.2262-0.028-0.00930.21890.02590.291727.917121.31054.1846
233.0686-0.2180.961.344-1.1143.88860.0345-0.0882-0.0149-0.0117-0.08440.1324-0.0078-0.01550.01540.20770.00570.04440.0853-0.0360.195638.708121.20799.2482
242.3734-0.01961.7263-0.0355-0.26392.7383-0.2326-0.24460.2807-0.0932-0.00220.0898-0.5128-0.33720.18290.29240.0657-0.010.1704-0.04650.231633.212925.48446.0572
251.87420.0281-0.35192.19070.45852.0405-0.17820.0980.0177-0.06590.12850.14280.4071-0.2030.01140.4331-0.048-0.08520.16390.05160.265819.445712.3033-23.8715
263.0590.91580.57841.91460.88538.474-0.0178-0.08470.2120.19940.06720.2199-0.4854-0.6322-0.04740.23680.02770.01540.21110.05320.305962.986316.396373.5822
272.89370.15220.57870.33110.21752.82980.1221-0.16770.06280.0094-0.0098-0.01080.26040.1421-0.14540.3660.0979-0.010.1894-0.01250.239984.944820.6712101.7357
284.49410.53252.83751.00721.72343.8486-0.01610.7175-0.6792-0.56430.4501-1.2368-0.6181.7903-0.08620.3811-0.2212-0.00840.6905-0.0250.420589.254116.28367.9394
291.74191.46921.2892.17832.4172.7321-0.15370.13460.2337-0.0285-0.01480.0391-0.40750.56180.13030.3098-0.19430.00480.42480.09170.350978.466517.895862.8362
303.17811.45472.41011.4320.98531.8657-0.38970.83981.0006-0.07990.4654-0.5037-1.18131.2470.09060.8839-0.5575-0.1910.5010.15170.624280.001728.043458.8008
311.5655-0.00111.50690.94281.45483.093-0.73550.74590.5598-0.30460.61480.1083-0.76691.34440.13510.3389-0.228-0.03560.65060.04610.380486.060719.593767.4448
321.07290.0179-0.93173.6701-1.13492.7350.29390.2352-0.1840.3310.3401-0.26530.94330.5385-0.21550.42170.2624-0.16510.4709-0.16640.299795.389811.324397.8676
332.3324-0.0286-0.80621.8257-1.03923.2922-0.02620.031-0.29850.39610.32260.21610.49390.1891-0.23840.56450.2079-0.11420.3779-0.18120.435292.78599.111895.5638
341.3333-0.1072-0.18383.1844-1.57193.6250.1714-0.41730.04460.2016-0.0043-0.74380.31271.45670.2080.69930.3407-0.05780.7996-0.20170.6372103.68497.11796.9239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 30 through 40 )
2X-RAY DIFFRACTION2chain 'C' and (resid 41 through 49 )
3X-RAY DIFFRACTION3chain 'C' and (resid 50 through 71 )
4X-RAY DIFFRACTION4chain 'C' and (resid 72 through 82 )
5X-RAY DIFFRACTION5chain 'C' and (resid 83 through 99 )
6X-RAY DIFFRACTION6chain 'C' and (resid 100 through 127 )
7X-RAY DIFFRACTION7chain 'C' and (resid 128 through 139 )
8X-RAY DIFFRACTION8chain 'C' and (resid 140 through 147 )
9X-RAY DIFFRACTION9chain 'D' and (resid 28 through 40 )
10X-RAY DIFFRACTION10chain 'D' and (resid 41 through 55 )
11X-RAY DIFFRACTION11chain 'D' and (resid 56 through 82 )
12X-RAY DIFFRACTION12chain 'D' and (resid 83 through 99 )
13X-RAY DIFFRACTION13chain 'D' and (resid 100 through 118 )
14X-RAY DIFFRACTION14chain 'D' and (resid 119 through 127 )
15X-RAY DIFFRACTION15chain 'D' and (resid 128 through 139 )
16X-RAY DIFFRACTION16chain 'D' and (resid 140 through 147 )
17X-RAY DIFFRACTION17chain 'H' and (resid 2 through 15 )
18X-RAY DIFFRACTION18chain 'H' and (resid 16 through 81 )
19X-RAY DIFFRACTION19chain 'H' and (resid 82 through 98 )
20X-RAY DIFFRACTION20chain 'H' and (resid 99 through 189 )
21X-RAY DIFFRACTION21chain 'H' and (resid 190 through 217 )
22X-RAY DIFFRACTION22chain 'L' and (resid 1 through 18 )
23X-RAY DIFFRACTION23chain 'L' and (resid 19 through 53 )
24X-RAY DIFFRACTION24chain 'L' and (resid 54 through 118 )
25X-RAY DIFFRACTION25chain 'L' and (resid 119 through 216 )
26X-RAY DIFFRACTION26chain 'A' and (resid 2 through 111 )
27X-RAY DIFFRACTION27chain 'A' and (resid 112 through 217 )
28X-RAY DIFFRACTION28chain 'B' and (resid 1 through 18 )
29X-RAY DIFFRACTION29chain 'B' and (resid 19 through 53 )
30X-RAY DIFFRACTION30chain 'B' and (resid 54 through 66 )
31X-RAY DIFFRACTION31chain 'B' and (resid 67 through 118 )
32X-RAY DIFFRACTION32chain 'B' and (resid 119 through 155 )
33X-RAY DIFFRACTION33chain 'B' and (resid 156 through 193 )
34X-RAY DIFFRACTION34chain 'B' and (resid 194 through 216 )

+
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