[English] 日本語
Yorodumi
- PDB-9nyz: Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nyz
TitleCrystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with UCM-101
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsMEMBRANE PROTEIN / ligand-gated ion channel allosteric modulation NMDA receptor synaptic protein neurotransmitter receptor
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication ...regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / auditory behavior / positive regulation of Schwann cell migration / olfactory learning / response to hydrogen sulfide / response to other organism / cellular response to magnesium ion / dendritic branch / conditioned taste aversion / response to methylmercury / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / regulation of respiratory gaseous exchange / response to manganese ion / transmitter-gated monoatomic ion channel activity / suckling behavior / sleep / positive regulation of inhibitory postsynaptic potential / response to carbohydrate / cellular response to dsRNA / cellular response to lipid / propylene metabolic process / response to glycine / regulation of NMDA receptor activity / dendritic spine organization / RAF/MAP kinase cascade / locomotion / response to amine / neurotransmitter receptor complex / Synaptic adhesion-like molecules / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / glutamate receptor signaling pathway / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / response to morphine / regulation of dendrite morphogenesis / male mating behavior / protein heterotetramerization / regulation of synapse assembly / spinal cord development / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / dopamine metabolic process / response to lithium ion / cellular response to zinc ion / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / regulation of postsynaptic membrane potential / monoatomic cation transmembrane transport / action potential / positive regulation of calcium ion transport into cytosol / cellular response to glycine / associative learning / positive regulation of dendritic spine maintenance / modulation of excitatory postsynaptic potential / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / monoatomic cation transport / glutamate receptor binding / conditioned place preference / prepulse inhibition / social behavior / ligand-gated monoatomic ion channel activity / neuron development / multicellular organismal response to stress / long-term memory / phosphatase binding / postsynaptic density, intracellular component / response to fungicide / monoatomic cation channel activity / synaptic cleft / calcium ion homeostasis / positive regulation of synaptic transmission, glutamatergic / cellular response to manganese ion / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / cell adhesion molecule binding / sensory perception of pain
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
: / 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID / GLUTAMIC ACID / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsLotti, J.S. / Syrenne, J.T. / Yates-Hansen, C.K. / McClelland, L.J. / Hansen, K.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097536 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 United States
CitationJournal: J.Gen.Physiol. / Year: 2026
Title: Novel binding mode for negative allosteric NMDA receptor modulators.
Authors: Lotti, J.S. / Syrenne, J.T. / Benton, A.J. / Al-Mousawi, A. / Cornelison, L.E. / Trolinder, C.J. / Yi, F. / Zhang, Z. / Yates-Hansen, C.K. / McClelland, L.J. / Bosco, J. / Rau, A.R. / ...Authors: Lotti, J.S. / Syrenne, J.T. / Benton, A.J. / Al-Mousawi, A. / Cornelison, L.E. / Trolinder, C.J. / Yi, F. / Zhang, Z. / Yates-Hansen, C.K. / McClelland, L.J. / Bosco, J. / Rau, A.R. / Clausen, R.P. / Hansen, K.B.
History
DepositionMar 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9355
Polymers65,1252
Non-polymers8103
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.474, 88.329, 137.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33340.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A


Mass: 31785.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959

-
Non-polymers , 4 types, 500 molecules

#3: Chemical ChemComp-DK1 / 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID / DCKA / 5,7-DICHLOROKYNURENIC ACID


Mass: 258.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H5Cl2NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#4: Chemical ChemComp-A1B7E / N-(cyclohexylmethyl)-2-[(5-{[(1R)-1-phenylpropyl]amino}-1,3,4-thiadiazol-2-yl)sulfanyl]acetamide


Mass: 404.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.71→33.28 Å / Num. obs: 71610 / % possible obs: 99.37 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.14
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.93 / Num. unique obs: 7030 / CC1/2: 0.376

-
Processing

Software
NameVersionClassification
autoPROCdata processing
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→33.28 Å / SU ML: 0.2221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2019 1999 2.79 %
Rwork0.1683 69571 -
obs0.1692 71570 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.96 Å2
Refinement stepCycle: LAST / Resolution: 1.71→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 0 53 497 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124763
X-RAY DIFFRACTIONf_angle_d1.12756457
X-RAY DIFFRACTIONf_chiral_restr0.0656705
X-RAY DIFFRACTIONf_plane_restr0.012835
X-RAY DIFFRACTIONf_dihedral_angle_d6.9578656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.32511410.30424907X-RAY DIFFRACTION98.65
1.76-1.80.31741400.28814885X-RAY DIFFRACTION99.66
1.8-1.860.32391390.26524866X-RAY DIFFRACTION99.07
1.86-1.920.32261410.26574911X-RAY DIFFRACTION99.12
1.92-1.980.28121420.24414906X-RAY DIFFRACTION99.35
1.98-2.060.28961410.21264931X-RAY DIFFRACTION99.43
2.06-2.160.22571420.18284929X-RAY DIFFRACTION99.33
2.16-2.270.20461420.17684949X-RAY DIFFRACTION99.36
2.27-2.410.21491430.15834956X-RAY DIFFRACTION99.75
2.41-2.60.18761440.16054999X-RAY DIFFRACTION99.67
2.6-2.860.19781430.16554993X-RAY DIFFRACTION99.65
2.86-3.280.19411430.17144998X-RAY DIFFRACTION99.44
3.28-4.130.17971460.14465059X-RAY DIFFRACTION99.39
4.13-33.280.16481520.13765282X-RAY DIFFRACTION99.63
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)
10.30928980763-0.22903203640.1202120921011.147799184890.9479874749981.14691496791-0.3019244889-0.381252264451-0.383623912779-0.0511517973484-0.111015220542-0.4691914239030.1464238822650.60834392634-0.007412789784350.2719931622970.014095209516-0.01382802972760.346186367221-0.01214495697910.4240522816376.73979952459-8.0400098466937.0170538158
20.5736159455550.4533725184360.6236987633010.531793771110.7252735052830.9864991141340.24434978159-0.644255640479-0.592107809280.3409085797160.0376699735534-0.009695279185810.442930817028-0.00679025361146-0.0003798993364910.3262343794720.0067231309883-0.04168103197940.3352043853020.01075434224430.3341437829163.80366710754-21.001679437745.9813522848
31.41947307018-0.120758724224-0.737484690530.287298457553-0.4126533494911.728844197350.09993858638310.115370729684-0.834345769574-0.22892381221-0.2431447114390.1559261413930.796195451599-0.65123249488-0.01702643796770.426848046673-0.0628347503032-0.01018101917590.244388229832-0.0523159449570.3843941928585.04409930095-26.970285504739.4829304881
40.1139332104760.0300583910557-0.1392283415860.1147315511660.08064358057230.294768388932-0.286528948186-0.1268314580240.1296485716180.960234024876-0.3919163906111.281367653220.0439999284367-0.365492550482-0.006350793555920.706108142346-0.001626656757380.1383246121230.454310129715-0.1639106888730.8628728691863.46964905617-6.283773566854.7885147433
50.9525906245050.14013483315-0.01081706526020.575210724303-0.6543167587720.7673468693830.002167520294320.01137466380670.112758014859-0.04524298211760.0144859457297-0.112639604469-0.00258038843854-0.056468746176-0.0002663310894890.2759128762190.00763082752816-0.02079901206960.245560634591-0.02411480963020.3364205115343.8221809051-17.080232687738.2510241089
60.9331004266090.1055219225750.480451185550.657044028882-0.07624990654190.88909894005-0.2348436453940.234748697353-0.02074508486920.02702231145470.0234356293196-0.2611346114850.2537549026070.01538551706950.0001895539171320.311306556272-0.03808290294280.01478211719220.33250857418-0.02865959561870.3505507575167.00914154192-10.675921850334.5419322149
71.22394901914-0.2227138670970.2035479556820.0672977924167-0.2385020761291.59045708936-0.0795251011387-0.1643651787751.051729115150.828607279884-0.0831729077196-0.0387633546064-1.36117496189-0.493438037308-0.004866019383030.9071919493010.193586299496-0.03506677846430.584413108287-0.1188638971720.66479374159-8.700854323638.1157095024844.748206659
81.468145311340.1250103184890.6174822794741.741348646790.6017779131461.81563623662-0.0827619483504-0.143832043410.1780054023270.0292279834718-0.05145985147360.00807409590435-0.173291887044-0.169621919751-7.44848483663E-50.2467562206350.0235787175761-0.02639716247430.196871979003-0.04467077577310.267522248148-5.82880933499-3.7902440497733.8691305521
94.617871048070.1678920077261.845206729940.0416479967154-0.09896365211231.510169212770.1129452515160.611597748801-1.230130784420.00374748591981-0.1091504557360.09531554797440.330438032339-0.5086313433960.0007890936102160.360503835099-0.01323762269030.02330519001290.565951455094-0.08939815844320.452650143633-29.4602048034-21.789600196741.5217414607
101.61335331362-0.302489829242-1.37228411870.4652170518070.2759570392381.167368286230.254401003612-0.05927879604950.2545675815130.01979972765030.2007792197690.0666132056238-0.491167420389-0.294972457380.01315858936650.476863800288-0.01771209789420.03968762942960.595823629505-0.08547268635350.347172149654-27.3999193885-9.3400369926645.4948910552
113.162529344311.10333178653-0.4239139652671.97156470090.303631477293.41088071540.0952012003644-0.676170450113-0.2557708175850.121811950869-0.17193020344-0.0189767881068-0.4291053160870.198963197492-0.002229341354890.374019191797-0.0397969816083-0.01368260191490.5711088252580.008509887717490.313397006536-22.1505792016-15.968340029247.8793475888
120.7186756234070.0806618911373-0.1807623070460.3965080525070.287659075880.825050343134-0.1916770658650.202476603009-0.529924853503-0.231064051580.2836082972630.1837172936510.304689060051-0.1275972117728.06660391279E-50.3807559300960.0141416333518-0.03183828323320.499436680538-0.02322097825250.486268885411-23.0637947465-21.208379742938.9203825137
130.918292885231-0.8756874122660.3342997973211.100642347040.3627776511661.86797793499-0.2315767258960.3099079494360.580677404717-0.4969331695240.03481524731780.230701368366-0.256519313424-0.252871132872-0.0007761065530410.3386852923530.0251101271796-0.04238650236310.240156293352-0.04045120153850.358477903544-5.36136640148-4.1670498658129.6753447119
141.04627218876-0.338186117341-0.3133660089310.485974680750.1980342965051.583075209970.158101982130.3085992221380.2042661759960.1474602539060.0965587492465-0.279651387602-0.3356065687050.161722955491-0.0004085622647130.359982453416-0.03027344161390.0227537122670.308873499868-0.0445331683440.359428565414-0.117869631567-10.140699173621.8617608194
150.18279476903-0.01208827076510.7229483452890.3009185525720.3175172027673.979329607820.0548916862216-0.0564049804539-0.4173071375930.0708885303980.01688648770150.3733909117860.826517230617-0.741502728372-0.07486716065350.2997177146140.00404663889308-0.02870932358790.2354343122540.008292453037310.355811634711-5.33646342302-24.542496425127.0970730451
160.396023850056-0.886841266992-1.150151485424.140185854161.510838593.86695235679-0.7101597573880.34994618222-1.094356628870.06107986339-0.01359918354381.401083706130.762147205543-1.18500502024-0.1355524102610.446229262217-0.0494793732830.06504829830350.466810032128-0.05784521872710.566501128529-8.82274877096-27.51359290737.0179186011
171.29450634089-0.130486157942-0.8390683467770.6470218940810.1113029089542.44338370099-0.0292152960469-0.09573803652620.269056104035-0.333679185814-0.02752913399230.501718349363-0.246325381753-0.464214361044-0.03853073815340.3264829414680.0535631406061-0.09610576007420.343042689887-0.06134862428580.375682304569-29.4219914984-3.797455041777.42544948862
180.0189219136635-0.1110466942510.1419269731181.316713517750.5733126384914.24424660948-0.3457574348080.15696476621-0.0742710343860.108298093243-0.1889170032960.717289893171-0.63138758369-1.46693831713-0.1289597616260.4092472209130.125508058146-0.05145621475460.501408300019-0.06413683230080.452774426465-33.4015979912-1.415661344695.22465375142
191.045776909810.0511941282140.5838067733550.610662122831-0.4769133674790.7558011638230.2560806152030.3435352560750.0586806498394-0.388674367175-0.113814941825-0.680828711281-0.3483985291540.05636146495570.003344340628330.402256297683-0.02261666472210.02624675128440.2838442173680.0241026386180.395560708098-27.7624877698-6.91914744835-10.9784698107
201.072084881570.841076773281-0.1416540926540.686529417379-0.2125188914990.366792065691-0.131467504487-0.1021086528870.155980302433-0.0536532579870.09536223827850.254667218708-0.357461399266-0.43733660475-0.0004173551671270.3874942470380.0700194115488-0.06000038739230.362230083282-0.07305026924990.358571365407-26.52278047950.71128143722914.3318096845
210.554438146773-0.3010262492010.1218069702780.3090148871660.1667996133410.393003071335-0.08682752992050.106709770264-0.350493581411-0.0791511628777-0.0946855122480.230540876579-0.0352888406176-0.112091048492-0.0005620997727860.29282291418-0.00033783969217-0.0133688450540.268019870659-0.02386691997190.267186019694-17.8861205511-10.87616642782.48108550279
221.25430530187-0.1232472782120.2856414947631.031805764960.2500004675911.21290772482-0.050977227565-0.1363901561760.1108694132850.02093495569960.014552710414-0.183363633969-0.0986401800009-0.04489780671929.09934716817E-50.217739223954-0.009461742129190.002214051571750.194881875396-0.02833074544620.229401428854-14.231407457-12.650015763811.6709209658
230.680655484809-0.212592904108-0.01717314837620.4121774478930.3178355742880.3059932026860.268961928491-0.930329458893-0.7268546278330.2890145361230.05782129190930.01382379085460.477160933832-0.1831701709720.007812828732970.4293664163160.0283275244067-0.004272997508270.4963660965770.05895977771110.404388045681-13.2375293628-36.064529587120.1759051158
242.03245711621-0.4807436959160.1444192598280.425762146477-0.4546952218481.194868491620.113098318602-0.11112137578-0.762403387599-0.4081382823620.03323212529810.2300904042990.597727392008-0.07403176664730.02346839785690.427657019944-0.0336862049323-0.03367243444910.2676220899280.01248055487650.347615519367-15.0048888056-38.154232350711.0999738943
250.74000338991-0.706773834132-0.3887326547780.6729543714990.3710407325290.203362124270.09362387901420.1451720517130.145755959839-0.3699685499610.0264350904696-0.165536918306-0.1393444149330.154922490025-7.34192618031E-50.356009677528-0.004408673663420.005177617514830.288732137595-0.02427371357890.278110703038-9.04358063773-28.482796970510.1086188481
260.299615061253-0.0466217308146-0.4855559317321.090401907420.1033403913160.783578908952-0.01225946229520.2858745456330.0931082377616-0.424211273585-0.02888385258560.2903709214910.246571106372-0.368653207742-0.0004536997089010.3551362012-0.0305690259359-0.05598778660.306023611546-0.02168345304970.2944230207-25.1045452839-31.1841886437.75254665912
271.175628375750.657845621787-0.1021947369211.279483346410.1442230520241.07976934841-0.13455699642-0.22562522755-0.1304374410210.2072086385810.1057045616880.5383991895320.370752828725-0.303060088496-0.003429955489390.23614278116-0.0485316009261-0.002987985251740.3099751384140.009280831510640.266522605082-27.2933489302-25.119800440217.4178606745
280.280580370663-0.123131524233-0.03884279725170.273618140215-0.099920233620.2926594718280.0285432516692-0.196590690965-0.4948155473670.413687369112-0.06558716224070.2848536098680.530174808552-0.2532888735290.004258456988260.384852840224-0.01057537330890.0505769690610.4589229440590.03258873392880.338676968362-25.8338654835-30.082161481823.2159342195
291.23473598209-0.7519021356340.08462364448251.144837894980.5951856315981.1003510333-0.0107101143235-0.2755058409460.07637534605570.1548933380980.0673552897009-0.3439590551050.01573227073210.1340477038150.0002075739127570.288591378071-0.044771173032-0.02165070967870.284382900246-0.05477601771180.296906397041-12.9540198163-11.202840167217.6944601061
300.277562688210.4188405148120.1996559147120.881341988164-0.003514157109240.510687204418-0.0214934211366-0.3595170781730.388706276808-0.1085119508460.01354232587180.198556836954-0.2651202085250.1674817277120.0001409168852240.3443307773580.0181510192215-0.03981001814790.341914056258-0.08619440623150.355012950965-16.84894298451.7972275058424.0327319074
310.215689983017-0.5111782127880.3626992419891.63504955672-1.108324069590.756145909277-0.484652759352-1.867694328460.6643054427631.385607753240.3752527467650.0734941298776-0.411644502318-0.5334725921120.01840563191970.4875256286480.118561300223-0.02268096872560.882693909177-0.08538635626420.507166328235-28.6851695871-6.6749110090726.6003444292
322.18754063844-2.17547465796-1.991994566167.564586802457.096918163556.66167382061-0.399117311496-0.534136202913-0.8608211581041.490844992690.3583733428880.7765778641141.6509957894-0.3003004735940.2879417789970.380618864336-0.05309115846950.07118874035690.471483920995-0.009454484134790.394546957887-32.372989323-18.981585396825.0945515155
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 3:12)AA3 - 121 - 10
22(chain A and resid 13:29)AA13 - 2911 - 27
33(chain A and resid 30:44)AA30 - 4428 - 42
44(chain A and resid 45:57)AA45 - 5743 - 55
55(chain A and resid 58:74)AA58 - 7456 - 72
66(chain A and resid 75:90)AA75 - 9073 - 88
77(chain A and resid 91:105)AA91 - 10589 - 103
88(chain A and resid 106:146)AA106 - 146104 - 144
99(chain A and resid 147:162)AA147 - 162145 - 160
1010(chain A and resid 163:189)AA163 - 189161 - 187
1111(chain A and resid 190:235)AA190 - 235188 - 233
1212(chain A and resid 236:246)AA236 - 246234 - 244
1313(chain A and resid 247:257)AA247 - 257245 - 255
1414(chain A and resid 258:272)AA258 - 272256 - 270
1515(chain A and resid 273:283)AA273 - 283271 - 281
1616(chain A and resid 284:287)AA284 - 287282 - 285
1717(chain B and resid 6:29)BE6 - 291 - 24
1818(chain B and resid 30:42)BE30 - 4225 - 37
1919(chain B and resid 43:56)BE43 - 5638 - 51
2020(chain B and resid 57:79)BE57 - 7952 - 74
2121(chain B and resid 80:92)BE80 - 9275 - 87
2222(chain B and resid 93:144)BE93 - 14488 - 139
2323(chain B and resid 145:155)BE145 - 155140 - 150
2424(chain B and resid 156:171)BE156 - 171151 - 166
2525(chain B and resid 172:188)BE172 - 188167 - 183
2626(chain B and resid 189:208)BE189 - 208184 - 203
2727(chain B and resid 209:229)BE209 - 229204 - 224
2828(chain B and resid 230:236)BE230 - 236225 - 231
2929(chain B and resid 237:254)BE237 - 254232 - 249
3030(chain B and resid 255:270)BE255 - 270250 - 265
3131(chain B and resid 271:278)BE271 - 278266 - 273
3232(chain B and resid 279:286)BE279 - 286274 - 281

+
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