[English] 日本語
Yorodumi
- PDB-7ta6: Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ta6
TitleTrimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1
Components
  • Alpha/Beta-peptide-1
  • Tumor necrosis factor
KeywordsSIGNALING PROTEIN / tumor necrosis factor-alpha / signaling
Function / homology
Function and homology information


negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / : ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / : / positive regulation of vitamin D biosynthetic process / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / response to isolation stress / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / cellular response to toxic substance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / sequestering of triglyceride / positive regulation of interleukin-18 production / positive regulation of action potential / TNF signaling / positive regulation of protein transport / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / positive regulation of superoxide dismutase activity / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / negative regulation of glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / negative regulation of oxidative phosphorylation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / regulation of synapse organization / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of interleukin-6 production / phagocytic cup / antiviral innate immune response / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / skeletal muscle contraction
Similarity search - Function
Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
: / AMINO GROUP / Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsNiu, J. / Bingman, C.A. / Gellman, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056414 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Trimer-to-Monomer Disruption Mechanism for a Potent, Protease-Resistant Antagonist of Tumor Necrosis Factor-alpha Signaling.
Authors: Niu, J. / Cederstrand, A.J. / Eddinger, G.A. / Yin, B. / Checco, J.W. / Bingman, C.A. / Outlaw, V.K. / Gellman, S.H.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 2.0Feb 15, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_asym / struct_conf / struct_conn / struct_ref_seq
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
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_atom_id / _atom_site.label_atom_id
Revision 3.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor
D: Tumor necrosis factor
E: Tumor necrosis factor
F: Tumor necrosis factor
G: Tumor necrosis factor
H: Tumor necrosis factor
I: Alpha/Beta-peptide-1
J: Alpha/Beta-peptide-1
K: Alpha/Beta-peptide-1
L: Alpha/Beta-peptide-1
M: Alpha/Beta-peptide-1
N: Alpha/Beta-peptide-1
O: Alpha/Beta-peptide-1
P: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,67633
Polymers166,01316
Non-polymers66417
Water81145
1
A: Tumor necrosis factor
N: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9546
Polymers20,7522
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor necrosis factor
I: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8304
Polymers20,7522
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tumor necrosis factor
J: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8925
Polymers20,7522
Non-polymers1403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tumor necrosis factor
K: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8304
Polymers20,7522
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tumor necrosis factor
M: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8304
Polymers20,7522
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tumor necrosis factor
L: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7683
Polymers20,7522
Non-polymers161
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Tumor necrosis factor
O: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7683
Polymers20,7522
Non-polymers161
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Tumor necrosis factor
P: Alpha/Beta-peptide-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8074
Polymers20,7522
Non-polymers552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.774, 143.552, 76.888
Angle α, β, γ (deg.)90.000, 97.850, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Protein/peptide , 2 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


Mass: 17457.736 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01375
#2: Protein/peptide
Alpha/Beta-peptide-1


Mass: 3293.842 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

-
Non-polymers , 4 types, 62 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5
Details: 0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2.67→101.11 Å / Num. obs: 43735 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 75.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Net I/σ(I): 9.5 / Num. measured all: 298842
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.67-2.8271.7894447963480.4280.7241.9311.1100
8.45-101.116.30.052894314110.9980.0220.05725.899.7

-
Processing

Software
NameVersionClassification
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
autoPROC20190923data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TNF_A

Resolution: 2.67→39.74 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 1997 4.57 %
Rwork0.2449 41695 -
obs0.2463 43692 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.26 Å2 / Biso mean: 101.43 Å2 / Biso min: 54.12 Å2
Refinement stepCycle: final / Resolution: 2.67→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10204 0 217 45 10466
Biso mean--92.87 73.89 -
Num. residues----1320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.740.38941000.34329993099100
2.74-2.810.35592000.336928973097100
2.81-2.90.3784990.337330223121100
2.9-2.990.33472000.329529073107100
2.99-3.10.32931000.320630243124100
3.1-3.220.35951850.300328943079100
3.22-3.370.28671150.282230263141100
3.37-3.540.37551000.287530093109100
3.54-3.770.30922000.256529313131100
3.77-4.060.32621000.243530403140100
4.06-4.460.26132000.203229143114100
4.46-5.110.2269990.196330333132100
5.11-6.430.26221990.231529393138100
6.43-39.740.18181000.22083060316099
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.5494-1.538-1.08072.8330.48034.08870.18220.0527-0.2818-0.45810.19390.25720.8911-0.15820.00021.0438-0.1094-0.25160.4820.05110.6778-38.91612.3869.163
24.3669-2.2788-1.09783.52351.4133.13630.00690.0638-0.50320.0619-0.2751.03760.0836-0.544300.5813-0.0233-0.01880.91440.05490.8805-59.37931.495-24.849
34.26952.1275-0.37812.9726-1.012.2215-0.0275-0.0494-0.79320.0111-0.1395-0.27530.30440.213600.8246-0.0086-0.03510.615-0.05290.7699-29.37312.944-25.266
44.24491.7934-1.36064.5327-1.74034.10330.02620.4037-0.3865-0.06210.2815-0.52530.09960.779500.5220.0044-0.0131.0089-0.29420.6991-11.32633.7739.177
53.0217-1.58910.90843.8123-0.64313.8341-0.1169-0.10250.5681-0.22140.1098-0.8165-0.1010.281600.5895-0.02990.01320.9255-0.04380.8078-11.81242.56-24.82
63.51321.81551.86133.16871.71933.8571-0.01750.34790.2617-0.06530.30030.246-0.1857-0.619500.50180.02630.06191.04210.24690.6745-60.31339.9228.632
73.4043-1.47990.97543.3912-1.33713.41170.44370.11740.6028-0.4580.001-0.3986-0.85290.11820.00111.1347-0.06560.35680.4761-0.03960.81-32.73761.3559.134
83.62860.83590.53552.9534-0.18773.3505-0.05280.4540.91240.1004-0.06930.4192-0.45540.033400.87890.09010.03450.56190.06310.8504-41.72260.716-25.065
90.7174-0.4557-0.3670.686-0.17110.29720.11221.06940.2136-1.0882-0.2227-0.64150.1419-0.2891-00.83720.0361-0.03760.9330.03580.7181-46.8333.993-34.212
100.5253-0.34510.50850.5215-0.49510.48520.68630.65460.406-0.1108-0.24710.58520.0108-0.418500.8129-0.02020.0510.7553-0.07070.8246-32.58126.078-33.98
110.51520.2452-0.46960.6456-0.1170.42740.2006-0.62850.44230.7020.29130.9862-0.390.3468-00.8013-0.06810.05840.81850.02030.8581-24.36935.3318.266
120.24870.2959-0.07950.5722-0.28390.20560.1388-0.1285-0.11520.30870.6313-0.901-0.46620.0233-0.00020.7922-0.04410.02540.84350.02690.7112-47.38338.45818.175
130.58910.02790.25690.61110.42630.32650.28161.0822-1.0288-0.5913-0.10051.2483-0.4640.23020.00770.85540.037-0.03231.0320.19440.8176-24.61139.926-34.344
141.205-0.22270.95260.55220.17490.73160.2022-0.45540.81170.14330.0696-0.6827-0.12180.14580.00010.7074-0.00620.00020.63970.02180.7325-37.72325.8717.611
150.8576-0.2282-0.7760.4392-0.29650.69670.7831-0.406-0.80310.274-0.32030.5487-0.2748-0.3316-00.8252-0.04540.11560.80030.0330.8913-34.03248.03417.835
160.6313-0.0407-0.06670.27960.22490.0881-0.09040.98220.1319-0.4262-0.1014-0.5694-0.2908-0.12340.00010.90560.0145-0.15191.0237-0.0250.922-38.8647.823-34.13
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:157 )A7 - 157
2X-RAY DIFFRACTION2( CHAIN B AND RESID 7:157 )B7 - 157
3X-RAY DIFFRACTION3( CHAIN C AND RESID 7:157 )C7 - 157
4X-RAY DIFFRACTION4( CHAIN D AND RESID 6:157 )D6 - 157
5X-RAY DIFFRACTION5( CHAIN E AND RESID 7:157 )E7 - 157
6X-RAY DIFFRACTION6( CHAIN F AND RESID 5:157 )F5 - 157
7X-RAY DIFFRACTION7( CHAIN G AND RESID 6:157 )G6 - 157
8X-RAY DIFFRACTION8( CHAIN H AND RESID 7:157 )H7 - 157
9X-RAY DIFFRACTION9( CHAIN I AND ( RESID 1:28 OR RESID 29:29 ) )I1 - 28
10X-RAY DIFFRACTION9( CHAIN I AND ( RESID 1:28 OR RESID 29:29 ) )I29
11X-RAY DIFFRACTION10( CHAIN J AND ( RESID 1:28 OR RESID 29:29 ) )J1 - 28
12X-RAY DIFFRACTION10( CHAIN J AND ( RESID 1:28 OR RESID 29:29 ) )J29
13X-RAY DIFFRACTION11( CHAIN K AND ( RESID 1:28 OR RESID 29:29 ) )K1 - 28
14X-RAY DIFFRACTION11( CHAIN K AND ( RESID 1:28 OR RESID 29:29 ) )K29
15X-RAY DIFFRACTION12( CHAIN L AND ( RESID 1:28 OR RESID 29:29 ) )L1 - 28
16X-RAY DIFFRACTION12( CHAIN L AND ( RESID 1:28 OR RESID 29:29 ) )L29
17X-RAY DIFFRACTION13( CHAIN M AND ( RESID 1:28 OR RESID 29:29 ) )M1 - 28
18X-RAY DIFFRACTION13( CHAIN M AND ( RESID 1:28 OR RESID 29:29 ) )M29
19X-RAY DIFFRACTION14( CHAIN N AND ( RESID 1:28 OR RESID 29:29 ) )N1 - 28
20X-RAY DIFFRACTION14( CHAIN N AND ( RESID 1:28 OR RESID 29:29 ) )N29
21X-RAY DIFFRACTION15( CHAIN O AND ( RESID 1:28 OR RESID 29:29 ) )O1 - 28
22X-RAY DIFFRACTION15( CHAIN O AND ( RESID 1:28 OR RESID 29:29 ) )O29
23X-RAY DIFFRACTION16( CHAIN P AND ( RESID 1:28 OR RESID 29:29 ) )P1 - 28
24X-RAY DIFFRACTION16( CHAIN P AND ( RESID 1:28 OR RESID 29:29 ) )P29

+
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://pdbjlvh1.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