[English] 日本語
Yorodumi
- PDB-4hre: Crystal Structure of p11/Annexin A2 Heterotetramer in Complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hre
TitleCrystal Structure of p11/Annexin A2 Heterotetramer in Complex with SMARCA3 Peptide
Components
  • Annexin A2
  • Helicase-like transcription factor
  • Protein S100-A10
KeywordsCalcium-binding protein / Calcium Binding / Nucleus
Function / homology
Function and homology information


negative regulation of formation of structure involved in a symbiotic process / bone sialoprotein binding / : / negative regulation by host of symbiont catalytic activity => GO:0052403 / Dissolution of Fibrin Clot / positive regulation of binding / body fluid secretion / small GTPase binding => GO:0031267 / macropinosome / positive regulation of low-density lipoprotein particle receptor binding ...negative regulation of formation of structure involved in a symbiotic process / bone sialoprotein binding / : / negative regulation by host of symbiont catalytic activity => GO:0052403 / Dissolution of Fibrin Clot / positive regulation of binding / body fluid secretion / small GTPase binding => GO:0031267 / macropinosome / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / Schmidt-Lanterman incisure / vesicle budding from membrane / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / response to thyroid hormone / plasma membrane protein complex / calcium-dependent phospholipid binding / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / ATP-dependent chromatin remodeler activity / positive regulation of low-density lipoprotein receptor activity / osteoclast development / extrinsic component of plasma membrane / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / positive regulation of focal adhesion assembly / basement membrane / regulation of neurogenesis / ATP-dependent activity, acting on DNA / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / ruffle / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / lipid droplet / helicase activity / positive regulation of GTPase activity / protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium channel activity / RING-type E3 ubiquitin transferase / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / ubiquitin protein ligase activity / positive regulation of fibroblast proliferation / melanosome / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / cell cortex / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / transmembrane transporter binding / early endosome / protein ubiquitination / endosome / positive regulation of protein phosphorylation / membrane raft / lysosomal membrane / DNA repair / ubiquitin protein ligase binding / calcium ion binding / nucleolus / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
Protein S100-A10 / HIRAN domain / HIRAN domain / HIRAN / Annexin A2 / Annexin / Zinc finger, C3HC4 type (RING finger) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin ...Protein S100-A10 / HIRAN domain / HIRAN domain / HIRAN / Annexin A2 / Annexin / Zinc finger, C3HC4 type (RING finger) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / EF-hand domain pair / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Annexin A2 / Protein S100-A10 / Helicase-like transcription factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7852 Å
AuthorsGao, P. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: SMARCA3, a Chromatin-Remodeling Factor, Is Required for p11-Dependent Antidepressant Action.
Authors: Oh, Y.S. / Gao, P. / Lee, K.W. / Ceglia, I. / Seo, J.S. / Zhang, X. / Ahn, J.H. / Chait, B.T. / Patel, D.J. / Kim, Y. / Greengard, P.
History
DepositionOct 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Annexin A2
C: Annexin A2
E: Protein S100-A10
F: Protein S100-A10
G: Helicase-like transcription factor
H: Helicase-like transcription factor
B: Annexin A2
D: Annexin A2
I: Protein S100-A10
J: Protein S100-A10
K: Helicase-like transcription factor
L: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)206,86112
Polymers206,86112
Non-polymers00
Water00
1
A: Annexin A2
C: Annexin A2
E: Protein S100-A10
F: Protein S100-A10
G: Helicase-like transcription factor
H: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)103,4316
Polymers103,4316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-89 kcal/mol
Surface area41470 Å2
MethodPISA
2
B: Annexin A2
D: Annexin A2
I: Protein S100-A10
J: Protein S100-A10
K: Helicase-like transcription factor
L: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)103,4316
Polymers103,4316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-91 kcal/mol
Surface area41380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.791, 74.346, 154.466
Angle α, β, γ (deg.)90.14, 96.56, 108.37
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Annexin A2 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / ...Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 38733.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anxa2, Anx2, Cal1h / Production host: Escherichia coli (E. coli) / References: UniProt: P07356
#2: Protein
Protein S100-A10 / Calpactin I light chain / Calpactin-1 light chain / Cellular ligand of annexin II / S100 calcium- ...Calpactin I light chain / Calpactin-1 light chain / Cellular ligand of annexin II / S100 calcium-binding protein A10 / p10 protein / p11


Mass: 11176.019 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A10, ANX2LG, CAL1L, CLP11 / Production host: Escherichia coli (E. coli) / References: UniProt: P60903
#3: Protein/peptide
Helicase-like transcription factor / DNA-binding protein/plasminogen activator inhibitor 1 regulator / HIP116 / RING finger protein 80 / ...DNA-binding protein/plasminogen activator inhibitor 1 regulator / HIP116 / RING finger protein 80 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3 / Sucrose nonfermenting protein 2-like 3


Mass: 1806.069 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
References: UniProt: Q14527, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ...References: UniProt: Q14527, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.7
Details: 0.1 M citric acid, 25% PEG 3350, pH 3.7, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7852→47.335 Å / Num. all: 50718 / Num. obs: 53292 / % possible obs: 95.17 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W7B and 4HRH

1w7b

4hrh


Resolution: 2.7852→47.335 Å / SU ML: 0.39 / σ(F): 1.96 / Phase error: 38.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2573 5.07 %RANDOM
Rwork0.249 ---
all0.2567 53292 --
obs0.2567 50718 95.17 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.583 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.6168 Å20.3397 Å211.8367 Å2
2---1.2062 Å23.1344 Å2
3----10.5623 Å2
Refinement stepCycle: LAST / Resolution: 2.7852→47.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14088 0 0 0 14088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814324
X-RAY DIFFRACTIONf_angle_d1.24119223
X-RAY DIFFRACTIONf_dihedral_angle_d17.9375509
X-RAY DIFFRACTIONf_chiral_restr0.0962108
X-RAY DIFFRACTIONf_plane_restr0.0052463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7852-2.83870.41051640.36572637X-RAY DIFFRACTION93
2.8387-2.89670.37921320.33942705X-RAY DIFFRACTION97
2.8967-2.95970.37871440.34092754X-RAY DIFFRACTION97
2.9597-3.02850.40381230.32342723X-RAY DIFFRACTION97
3.0285-3.10420.3731460.3082730X-RAY DIFFRACTION97
3.1042-3.18810.37241390.29922732X-RAY DIFFRACTION97
3.1881-3.28190.3461720.28162690X-RAY DIFFRACTION97
3.2819-3.38780.31511430.27012741X-RAY DIFFRACTION96
3.3878-3.50890.32591470.26692657X-RAY DIFFRACTION96
3.5089-3.64930.35871380.26192719X-RAY DIFFRACTION96
3.6493-3.81530.33281600.25682660X-RAY DIFFRACTION96
3.8153-4.01640.28621420.22972638X-RAY DIFFRACTION95
4.0164-4.26790.23531500.20582698X-RAY DIFFRACTION95
4.2679-4.59710.24341560.20132651X-RAY DIFFRACTION95
4.5971-5.05930.25611430.20762643X-RAY DIFFRACTION94
5.0593-5.79030.30041310.26222637X-RAY DIFFRACTION94
5.7903-7.29080.3211240.26262616X-RAY DIFFRACTION92
7.2908-47.34170.24471190.20952514X-RAY DIFFRACTION89
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)
10.3287-0.4464-0.29922.1751-1.51752.5294-0.4866-0.6650.01780.40060.3104-0.70720.83871.05930.48620.87390.0310.10790.80990.0760.488822.07657.1035-26.8372
21.9391-0.8811-1.39611.43761.03242.1441-0.0384-0.0406-0.16-0.0389-0.08940.1524-0.1193-0.01360.00060.28920.0260.06820.12570.05110.257718.15455.668-51.3894
31.5006-0.8267-0.9621.1033-0.35411.8004-0.34050.246-0.5255-0.83890.14160.44751.0716-0.35330.37660.7567-0.3306-0.10320.6873-0.01810.508615.8251.156716.9988
41.26730.4067-0.92661.7617-0.85981.6185-0.5402-0.1028-0.46570.44880.0964-0.18930.21060.1208-0.2727-0.1535-0.115-0.27910.3327-0.07760.148620.45671.347441.7844
55.83936.4863-0.93647.4189-1.43060.85570.1604-0.8284-0.90770.8331-0.5526-0.34450.21790.59440.23251.078-0.02590.12331.0744-0.08350.680527.4385-12.5322-1.272
60.67920.5908-0.13324.6585-0.80561.3570.63310.18930.45750.4362-1.1697-0.3977-0.2510.36390.38281.4343-0.6945-0.3591.41440.20661.456339.00830.2376-2.4127
73.45840.1514-2.73713.1896-1.77343.31210.0661-0.31450.7374-0.2592-0.4394-0.368-0.2310.89290.09051.01440.38160.35031.25480.4731.182337.5679-1.1232-12.5685
83.745-2.4633-1.25721.62190.86641.30690.041-1.0494-0.36050.27620.27280.05451.73510.0881-0.27061.64010.2142-0.00931.8917-0.08090.551330.7656-6.6051-19.4674
91.65630.5384-0.97744.0157-3.57963.34660.4069-0.28090.52320.6299-0.7947-0.3691-0.6817-0.08370.25110.96880.0390.24160.77750.25330.850532.42253.1403-21.4316
105.0412.24454.3058.15392.85323.89540.2118-0.82850.84660.27130.04240.3704-0.0396-0.0372-0.21610.8405-0.6072-0.06161.62250.09051.537429.79069.6428-6.6228
112.9186-0.2513-1.2123.2714-2.0471.92780.1710.3914-0.0857-0.2156-0.33060.34250.1945-0.293-0.12381.002-0.45390.0651.117-0.22890.426818.9134-5.1713-13.2559
122.3947-0.37780.26881.7251-0.88362.82110.08410.9295-0.5022-0.32950.26130.1920.5987-0.1407-0.05631.0751-0.3209-0.03040.75120.0170.723114.1224-14.5851-1.4543
131.38010.3241-0.63550.0786-0.14590.2961-0.0829-0.5374-0.34490.08670.65242.26870.7814-1.4221-0.59771.0937-0.09760.14181.52220.3231.26035.7973-6.34238.817
143.6158-0.58362.64837.1256-1.34312.67120.1409-0.21590.23540.9671-0.44410.5167-0.8105-0.87440.06681.0306-0.01850.47951.25170.2140.71755.2963-1.7823-2.2977
150.51120.0914-0.36660.4527-0.21430.31160.0687-0.03610.02520.2886-0.07090.0152-0.18430.1959-0.16381.548-0.70560.46280.8703-0.25480.528224.1908-5.55583.5614
160.0679-0.0197-0.09248.18311.7762.49530.2746-0.4720.13840.5051-0.5726-0.3356-1.2684-0.36760.19141.0055-0.11360.26491.08990.03850.865919.40753.6799-13.5509
177.1405-4.268.05772.7204-5.33952.00050.8592-1.2241-0.9772-0.430.39710.77251.7863-2.7477-1.36181.9508-0.60120.2331.4723-0.11930.609917.70.78425.0272
181.8673-1.7534-1.69892.17251.4371.7035-0.21690.6135-0.2375-0.8359-0.04290.31991.31830.0220.46290.8345-0.01840.0880.7992-0.03040.5223-5.786836.184193.8617
191.66970.2768-0.81862.3737-1.09590.8044-0.17370.303-0.125-0.20830.155-0.27860.1960.0690.03930.3581-0.01020.04530.2083-0.00840.3534.840146.8699.9438
202.781-0.7842-1.75522.0356-0.15633.3766-0.2044-0.0657-0.0535-0.0154-0.1337-0.11250.1850.0918-0.03060.5010.10570.1296-0.00930.06010.28061.368926.4908120.972
211.1910.7572-0.54262.7289-1.60462.03810.0568-0.105-0.00280.5804-0.07770.2268-0.26190.04820.02270.4970.1030.09210.2568-0.04690.3212-6.203339.6859126.2211
220.63190.2728-0.30081.1697-0.48410.7801-0.0193-0.7683-0.41590.67760.2769-0.42270.99730.4790.51610.7129-0.05050.03430.7208-0.19820.29773.106435.307449.6743
232.1651-0.4352-1.42491.29250.67062.26140.1269-0.015-0.0847-0.0517-0.13110.1136-0.3749-0.040.0050.037-0.0349-0.17620.21510.0190.2079-1.241733.458225.3246
240.1353-0.0925-0.28570.19210.40120.92960.33131.352-0.187-0.4502-0.5696-0.0394-0.0009-0.45160.16961.04340.1215-0.12690.90630.10630.7372-0.124317.714968.2118
257.9492-1.58556.22537.8285-0.20575.0149-0.2370.47980.1079-0.0215-0.39011.22790.3834-0.88640.35270.7379-0.39170.32271.68210.06371.185-14.57321.312575.82
264.1458-1.30962.87644.3205-3.80594.14470.06140.7193-0.6814-1.034-0.20810.52740.7015-0.2167-0.02381.11440.01010.13931.61340.01240.6446-8.642223.49789.6916
273.026-2.3988-1.12552.93212.20312.086-0.0034-0.10030.0149-0.1672-0.03390.3937-0.3308-0.6978-0.10910.6988-0.1025-0.03311.2188-0.03951.2677-13.63134.270276.0814
289.44260.60812.37843.78191.62095.3113-0.01870.45420.1570.1716-0.8762-0.36170.2860.4950.08990.8212-0.10930.11091.07310.21330.51973.719528.722880.4163
295.1440.84430.52863.2791-0.21967.91281.0053-0.6028-0.17430.72160.1484-0.95770.56821.089-0.13870.77150.0874-0.01670.7939-0.17750.869713.556923.713869.7159
300.688-1.7629-1.74296.56075.59785.03940.2067-0.0982-0.1024-0.04190.3517-0.2361-0.23950.7994-0.2260.9814-0.09250.46021.3352-0.01220.796514.008333.883856.684
313.84364.0074-2.2874.5468-2.61011.8877-0.5151-0.36281.1546-0.8036-0.2544-0.7037-0.9045-0.240.76671.5426-0.322-0.2341.4888-0.00440.872313.266640.068369.531
322.44362.61881.37245.43083.00086.04730.00150.8654-0.0364-0.834-0.32680.1976-0.2197-0.77490.04360.51990.11510.14331.24630.09370.1025-0.028226.154663.5933
334.50070.75963.86341.56971.85174.31340.80210.12420.0215-0.26740.25961.3273-1.5933-2.3509-1.11071.14020.17140.06170.96330.19821.0786-1.756236.033980.4864
341.95393.36252.89967.3856.50865.7414-0.07450.83690.1635-0.5018-0.15360.035-0.33011.6720.41660.93180.1374-0.08181.18620.41430.43341.745734.815462.1202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:40)
2X-RAY DIFFRACTION2chain 'A' and (resseq 41:339)
3X-RAY DIFFRACTION3chain 'C' and (resseq 2:41)
4X-RAY DIFFRACTION4chain 'C' and (resseq 42:339)
5X-RAY DIFFRACTION5chain 'E' and (resseq 1:15)
6X-RAY DIFFRACTION6chain 'E' and (resseq 16:26)
7X-RAY DIFFRACTION7chain 'E' and (resseq 27:37)
8X-RAY DIFFRACTION8chain 'E' and (resseq 38:42)
9X-RAY DIFFRACTION9chain 'E' and (resseq 43:55)
10X-RAY DIFFRACTION10chain 'E' and (resseq 56:67)
11X-RAY DIFFRACTION11chain 'E' and (resseq 68:91)
12X-RAY DIFFRACTION12chain 'F' and (resseq 1:47)
13X-RAY DIFFRACTION13chain 'F' and (resseq 48:56)
14X-RAY DIFFRACTION14chain 'F' and (resseq 57:67)
15X-RAY DIFFRACTION15chain 'F' and (resseq 68:91)
16X-RAY DIFFRACTION16chain 'G' and (resseq -2:6)
17X-RAY DIFFRACTION17chain 'H' and (resseq -2:6)
18X-RAY DIFFRACTION18chain 'B' and (resseq 2:38)
19X-RAY DIFFRACTION19chain 'B' and (resseq 39:118)
20X-RAY DIFFRACTION20chain 'B' and (resseq 119:198)
21X-RAY DIFFRACTION21chain 'B' and (resseq 199:339)
22X-RAY DIFFRACTION22chain 'D' and (resseq 2:39)
23X-RAY DIFFRACTION23chain 'D' and (resseq 40:339)
24X-RAY DIFFRACTION24chain 'I' and (resseq 1:17)
25X-RAY DIFFRACTION25chain 'I' and (resseq 18:37)
26X-RAY DIFFRACTION26chain 'I' and (resseq 38:51)
27X-RAY DIFFRACTION27chain 'I' and (resseq 52:67)
28X-RAY DIFFRACTION28chain 'I' and (resseq 68:91)
29X-RAY DIFFRACTION29chain 'J' and (resseq 1:44)
30X-RAY DIFFRACTION30chain 'J' and (resseq 45:56)
31X-RAY DIFFRACTION31chain 'J' and (resseq 57:67)
32X-RAY DIFFRACTION32chain 'J' and (resseq 68:91)
33X-RAY DIFFRACTION33chain 'K' and (resseq -2:6)
34X-RAY DIFFRACTION34chain 'L' and (resseq -2:6)

+
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