[English] 日本語
Yorodumi
- PDB-6axg: Structure of RasGRP4 in complex with HRas -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6axg
TitleStructure of RasGRP4 in complex with HRas
Components
  • GTPase HRasHRAS
  • RAS guanyl-releasing protein 4
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


diacylglycerol binding / GTP-dependent protein binding / regulation of G protein-coupled receptor signaling pathway / : / myeloid cell differentiation / GTPase complex / positive regulation of Ras protein signal transduction / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane ...diacylglycerol binding / GTP-dependent protein binding / regulation of G protein-coupled receptor signaling pathway / : / myeloid cell differentiation / GTPase complex / positive regulation of Ras protein signal transduction / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / small GTPase-mediated signal transduction / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / activation of phospholipase C activity / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / FCERI mediated NF-kB activation / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by RAF1 mutants
Similarity search - Function
Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases ...Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-hand calcium-binding domain profile. / EF-hand domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GTPase HRas / RAS guanyl-releasing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsKondo, Y. / Iwig, J.S. / Kuriyan, J.
CitationJournal: Elife / Year: 2017
Title: A histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1.
Authors: Vercoulen, Y. / Kondo, Y. / Iwig, J.S. / Janssen, A. / White, K.A. / Amini, M. / Barber, D.L. / Kuriyan, J. / Roose, J.P.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS guanyl-releasing protein 4
B: GTPase HRas
C: RAS guanyl-releasing protein 4
D: GTPase HRas
E: RAS guanyl-releasing protein 4
F: GTPase HRas
G: RAS guanyl-releasing protein 4
H: GTPase HRas
I: RAS guanyl-releasing protein 4
J: GTPase HRas
K: RAS guanyl-releasing protein 4
L: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)395,19512
Polymers395,19512
Non-polymers00
Water0
1
A: RAS guanyl-releasing protein 4
B: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)65,8662
Polymers65,8662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-9 kcal/mol
Surface area23630 Å2
MethodPISA
2
C: RAS guanyl-releasing protein 4
D: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)65,8662
Polymers65,8662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-9 kcal/mol
Surface area23670 Å2
MethodPISA
3
E: RAS guanyl-releasing protein 4
F: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)65,8662
Polymers65,8662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-8 kcal/mol
Surface area24150 Å2
MethodPISA
4
G: RAS guanyl-releasing protein 4
H: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)65,8662
Polymers65,8662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-6 kcal/mol
Surface area23720 Å2
MethodPISA
5
I: RAS guanyl-releasing protein 4
J: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)65,8662
Polymers65,8662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-7 kcal/mol
Surface area23560 Å2
MethodPISA
6
K: RAS guanyl-releasing protein 4
L: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)65,8662
Polymers65,8662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-7 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.105, 114.105, 680.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein
RAS guanyl-releasing protein 4


Mass: 46660.285 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASGRP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDF6
#2: Protein
GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 19205.596 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 and 300 mM sodium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.21 Å / Num. obs: 76133 / % possible obs: 98.7 % / Redundancy: 9.2 % / CC1/2: 0.968 / Rmerge(I) obs: 0.224 / Net I/σ(I): 8.3
Reflection shellResolution: 3.3→3.37 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.521

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4l9m

4l9m


Resolution: 3.302→49.21 Å / Cross valid method: FREE R-VALUE / σ(F): 105.97 / Phase error: 37.99
RfactorNum. reflection% reflection
Rfree0.2602 3814 5.06 %
Rwork0.2273 --
obs0.2295 76133 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.302→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23168 0 0 0 23168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323601
X-RAY DIFFRACTIONf_angle_d0.77631966
X-RAY DIFFRACTIONf_dihedral_angle_d6.94114207
X-RAY DIFFRACTIONf_chiral_restr0.0453631
X-RAY DIFFRACTIONf_plane_restr0.0054130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3025-3.35940.30492120.2843467X-RAY DIFFRACTION89
3.3594-3.42050.35811490.29863383X-RAY DIFFRACTION91
3.4205-3.48620.30731870.28843481X-RAY DIFFRACTION91
3.4862-3.55740.28652040.27263495X-RAY DIFFRACTION91
3.5574-3.63470.35591940.33485X-RAY DIFFRACTION92
3.6347-3.71920.37231890.34093527X-RAY DIFFRACTION93
3.7192-3.81210.31941880.24353656X-RAY DIFFRACTION94
3.8121-3.91510.35521350.28773634X-RAY DIFFRACTION96
3.9151-4.03030.26611980.23223612X-RAY DIFFRACTION95
4.0303-4.16030.23161860.22513603X-RAY DIFFRACTION95
4.1603-4.30880.24962010.21623644X-RAY DIFFRACTION95
4.3088-4.48120.22781820.20923672X-RAY DIFFRACTION95
4.4812-4.68490.21491610.19923683X-RAY DIFFRACTION96
4.6849-4.93160.23332120.19583662X-RAY DIFFRACTION95
4.9316-5.24010.25512040.20413644X-RAY DIFFRACTION95
5.2401-5.6440.25142010.2233673X-RAY DIFFRACTION95
5.644-6.21050.27671910.24393676X-RAY DIFFRACTION95
6.2105-7.1060.24792260.22793703X-RAY DIFFRACTION94
7.106-8.94050.2071900.17693732X-RAY DIFFRACTION95
8.9405-44.05520.21912030.19033861X-RAY DIFFRACTION95
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)
16.5943-0.06382.41.17880.48633.8783-0.2221-0.5892-0.31240.21720.25420.05230.0221-0.43190.05110.6920.5843-0.07261.1958-0.1790.1747326.9722479.7312745.8503
26.72081.60691.86548.16456.32536.7460.05870.75690.0677-1.56490.5085-0.0644-1.0271.3922-0.62281.34610.13310.14230.7334-0.07040.3709330.111481.9374740.7828
31.53661.65671.08542.20880.95320.8735-0.34540.5791-0.1776-0.2810.4071-0.2124-0.2294-0.1135-0.0571.35570.27720.05420.934-0.14230.3689318.3532489.7252742.9973
41.0585-1.56022.51813.4537-3.48526.61490.3045-0.1498-0.1057-0.01660.34040.6541-0.75420.7104-0.72080.75150.05460.15790.9299-0.15490.6074298.1701412.8235705.3308
52.7544-0.57180.85822.75881.27951.897-0.85111.4170.5776-0.2784-0.28120.47220.23680.41870.67090.58470.2126-0.23921.1964-0.15310.7275294.0131402.8103701.4444
61.0790.67480.89888.5366-2.06464.4222-0.8420.5293-0.0671-0.44380.20020.2743-0.08110.46210.44860.4897-0.18670.04240.674-0.28070.561302.4939396.3129700.2178
71.72050.3931-0.08540.6309-0.11110.19850.09970.0635-0.11280.05310.0069-0.0653-0.4358-0.2272-0.01771.18010.0071-0.03710.6293-0.29760.0188331.5218425.1972699.7701
81.5992-0.2332-0.01953.1816-1.26225.2909-0.21440.71810.2534-0.31790.25980.45720.7027-0.02220.09270.46540.0919-0.16071.0245-0.30440.5702310.7554421.1719708.2363
92.73830.53442.68432.5314-0.27442.8395-0.1580.0315-0.37440.23220.2209-0.4993-0.2468-0.03510.02210.57980.1430.04570.3602-0.14250.5928340.0187419.5365697.0105
103.82040.6493-0.3636.83631.07440.22690.04610.6902-0.0923-0.0264-0.15040.60470.8315-0.57760.02520.9999-0.1893-0.27570.6719-0.02780.2679320.0462429.6841723.9259
118.2947-2.6989-2.78957.0936-2.33782.6330.0738-0.57990.56871.25931.6022-0.85150.39910.5512-1.56280.6819-0.2459-0.26010.7854-0.04670.5264325.3421427.9748719.5603
120.48230.48590.12460.69220.25380.2569-0.01690.0904-0.19760.13860.2195-0.12610.04130.47540.24311.29820.3469-0.10311.052-0.2558-0.6656333.4364417.2589725.6876
131.3523-0.29471.57570.538-0.65272.0354-0.0915-0.44530.14230.48650.42110.27810.1614-0.1281-0.13591.0458-0.29690.53820.6462-0.25070.9494325.2135424.259733.8363
140.4506-0.1028-0.56440.28580.10052.73430.15260.4908-0.1799-0.25920.12060.7149-0.0486-1.17680.04770.35030.1534-0.62250.70640.13861.0604298.8553439.7875774.5754
151.1882-0.634-2.0775.6461-0.01974.8194-0.0286-1.0881-0.0760.369-0.3121-0.1381-0.59430.30790.28180.4964-0.28-0.11271.0437-0.03170.5376299.4717452.5396777.7166
162.6604-0.7965-0.06171.2112-0.59630.4985-0.108-0.14960.4445-0.26870.06620.23160.09810.02940.08550.9647-0.1455-0.00920.292-0.15250.4691327.2444438.3569781.0799
171.7888-0.46730.46321.19180.75151.9069-0.0374-0.1412-0.1087-0.23540.12430.1050.4369-0.1481-0.04570.7794-0.25950.02770.3786-0.01460.24331.5656425.9333775.7462
182.03031.2459-0.9693.4874-0.06340.64540.1694-0.2997-0.103-0.0529-0.75690.21530.502-0.54940.53630.8784-0.145-0.01870.67320.02040.473322.0858421.4099754.7116
190.104-0.09590.11620.1035-0.21471.5787-0.1775-0.10980.0873-0.04320.0326-0.014-0.11110.05550.01351.1903-0.24570.13051.0706-0.1869-0.3774333.1814433.9615755.7559
204.4664-3.68950.30284.91810.93895.83330.24570.94370.3747-0.6268-0.5251-0.3467-0.30860.49850.10291.0142-0.2624-0.23121.18710.04450.1811328.6802430.8666744.1674
210.56260.53360.32340.5442-0.04183.29690.3567-0.3456-0.41350.0161-0.0742-0.230.8164-0.1114-0.29360.7609-0.0644-0.12180.90440.37940.4502291.1643444.1315699.6749
224.2894-1.31361.10832.8445-0.46682.16210.52630.3190.4747-0.4225-0.4799-0.6457-0.01190.398-0.06370.40520.0850.06331.0788-0.01030.4066301.9865450.5741696.5054
233.5224-2.75190.72612.7329-0.10530.4420.5164-0.06260.4726-0.2958-0.298-0.3579-0.0306-0.1787-0.1330.6442-0.0770.18510.61110.08430.2851276.462465.8548692.8131
241.3057-0.3285-0.40462.2003-0.26041.02560.0199-0.02180.238-0.2170.10260.2798-0.0166-0.08160.11020.1155-0.29760.02330.37080.21350.6928256.9648474.6658696.7815
250.74840.488-0.74740.393-0.26082.18410.1231-0.3365-0.03030.2129-0.25740.07010.0531-0.05570.15390.55630.20310.28710.9630.1980.1038253.3616465.0091702.91
261.14110.28040.33740.8675-0.3310.5851-0.15640.0373-0.10230.1063-0.0080.18770.3361-0.18330.01360.5665-0.16890.16180.69150.0630.0176270.818462.905700.5656
271.62390.3125-1.32133.0607-0.79672.6234-0.14580.4819-0.0827-0.38620.1701-0.24540.18320.5690.01740.61460.23780.04090.77320.05450.1443266.5816458.3404720.9992
281.3576-0.2467-0.65593.8551-1.17261.28470.24870.32220.7349-0.47540.48990.845-0.1516-0.6547-0.71490.6797-0.02790.47270.90130.59131.5254267.3833447.5908714.7226
291.83640.43850.42284.876-1.00830.5348-0.09160.0864-0.3769-0.04550.33130.47170.6553-0.5258-0.14910.8382-0.42340.05150.966-0.08560.3613259.9911452.1792723.5433
301.9124-0.5268-3.08221.6481.19985.89180.2065-0.01310.237-0.2130.0244-0.3122-0.20550.7868-0.05130.5454-0.19520.02050.60370.1845-0.0119264.1634467.666710.5042
310.74640.04441.92272.85550.53665.0134-0.41540.59240.1637-0.12430.1758-0.1663-0.23120.43310.11470.54-0.16330.18760.75010.08550.2182271.3171466.7545723.6026
324.835-1.491.51371.4232-0.57430.4871-0.40090.2110.17420.1470.18360.2477-0.81770.790.15380.6314-0.17580.04870.6260.03410.2868268.8385475.6344720.438
336.3854-1.0794-0.57820.81960.1750.7393-0.0764-0.42830.94170.37330.017-0.03650.0061-0.16420.34940.69-0.54170.08341.1033-0.39370.3169271.3202472.1345730.2057
342.4985-2.1938-4.07495.16364.83937.1406-0.4464-0.2908-0.24250.73520.54990.26961.23890.7510.01491.1589-0.11220.1340.68050.10080.0978274.7774460.8638730.8655
351.37510.7673-0.21098.3366-2.24936.0170.1737-0.67040.50240.04350.14790.02150.46390.7124-0.38190.532-0.1917-0.05921.53210.03070.578261.4805460.1335730.7906
362.1415-0.10571.57920.3856-0.31511.84780.07140.3828-1.1152-0.23290.4354-1.395-0.54950.3351-0.53050.6284-0.04130.12150.5354-0.22650.9562266.1162426.9013773.7832
374.45660.4494-0.27980.6980.83261.16330.211-0.5990.04420.0140.104-0.8845-0.22390.1246-0.25030.34980.12570.4451.19470.07861.5279256.6657426.1779.4327
380.1877-0.49540.40983.20350.32871.2784-0.0947-0.06490.08860.24130.19080.0699-0.05510.7774-0.0540.3292-0.07030.10781.035-0.05850.3256258.0142463.3031778.8705
390.3411-0.22730.00360.7724-0.00260.7721-0.10070.0692-0.12950.18290.0553-0.0749-0.32940.35070.14680.7741-0.3530.2211.19480.0922-0.1209269.0009460.2986769.4946
401.50030.82660.69822.3831-0.91175.3001-0.13250.421-0.0319-0.1860.00850.42110.28330.3850.07010.2381-0.03880.08930.4826-0.15510.1144252.6787470.9716778.3116
411.2212-0.94641.15692.2960.06361.6764-0.0974-0.2051-0.09530.3739-0.233-0.20590.0453-0.14760.2260.908-0.06370.15680.72770.35050.1731267.293458.4699752.1708
420.6040.28020.03763.77891.0461.29320.10040.1241-0.3303-0.1031-0.0441-0.83340.07890.4893-0.03260.5705-0.05040.09851.16110.27310.2298270.4924460.4178756.6123
431.17031.0457-1.22621.6942-1.50731.5155-0.11830.1103-0.0267-0.30620.1950.0417-0.0540.00780.17020.754-0.2913-0.12820.74880.02-0.2446257.7302458.5719749.7631
440.60890.2485-0.1491.88961.37031.17190.1169-0.04890.00890.5047-0.21820.3745-0.1865-0.2843-0.01750.54190.09160.18760.8210.10490.116251.1404464.9318753.4758
450.0425-0.0441-0.15010.1640.62722.3802-0.0162-0.0386-0.0163-0.05190.09140.039-0.6373-0.32690.09410.5849-0.2739-0.10211.11510.1344-0.0504257.9381467.2058747.1104
460.431-0.56940.73811.8074-0.57351.41610.12160.5371-0.336-0.72570.18751.67380.3993-0.6308-0.23720.4435-0.2226-0.28521.2074-0.14360.8484253.8281455.7196741.584
478.6992-6.6984-1.71075.97481.99682.6616-0.21120.42720.4782-0.85570.1724-1.4013-0.41170.7992-0.07420.4796-0.41570.04211.15750.09590.5104268.088463.5389742.3916
483.14111.6288-1.74871.3122-1.18722.19760.1-0.48480.64380.22220.2091-0.1959-0.24910.7625-0.03320.9935-0.1588-0.66640.8231-0.25541.169323.2637521.0046704.4687
491.12460.88880.19572.7217-0.04380.3651-0.28970.4335-0.0716-0.61850.3825-0.3950.2822-0.157-0.0660.6121-0.8766-0.07470.89-0.09621.0019312.1532528.5805699.7564
500.78180.0455-0.6162.23580.19380.66970.0937-0.00770.3532-0.1125-0.05660.0938-0.174-0.04180.17380.423-0.1295-0.26241.1980.30070.2383311.0481495.5149695.1993
511.38490.31190.78920.98720.74761.823-0.1839-0.06440.13230.3487-0.071-0.21480.00470.70380.25620.3248-0.1427-0.0411.3771-0.04070.4737322.1429477.0424699.1493
522.0672-0.16710.25541.2788-1.10771.0826-0.1197-0.00990.00790.30250.3184-0.4097-0.60930.57880.0110.4351-0.12670.00341.3770.14870.5113324.4463505.7691706.11
530.3458-0.46990.00621.8847-1.19584.18810.0292-0.33790.033-0.038-0.22450.3057-0.4110.26170.1490.366-0.05990.09181.1293-0.25670.0964307.4706481.3313694.8657
542.3510.21071.65830.6345-0.08951.27-0.70590.57360.6477-0.5790.1254-0.05980.12380.23850.34980.936-0.3071-0.0821.03540.12190.5004328.3615494.2913720.0225
550.14620.2735-0.07260.92540.9182.57560.08890.070.0504-0.1360.2105-0.0722-0.12170.1602-0.00040.7347-0.18950.04861.41770.083-0.0528321.6867486.5389715.5913
560.6722-0.11550.39260.38570.28520.6215-0.07320.1133-0.24730.0873-0.0069-0.0041-0.2634-0.1243-0.04650.7623-0.2356-0.08771.33870.08610.1166310.8191486.5526722.8466
573.45410.6568-2.9031.4112-0.09263.32320.1218-0.2518-0.8660.0141-0.16270.10660.0677-0.06490.03130.38020.07480.31490.98440.04561.4295305.9222492.529733.1074
580.49880.95730.01293.5614-1.37141.1256-0.1478-0.39060.20720.8383-0.1791.0396-0.3668-0.98070.1441.0280.14340.14551.4883-0.45480.5524317.0775497.1645731.5887
590.9097-1.6070.91459.8801-2.87571.1445-0.185-0.9039-0.15831.13080.25480.0242-0.29310.1363-0.03490.77890.46210.161.4964-0.15210.5686324.5026486.1665730.7863
602.79432.0040.67762.32880.52580.218-0.3950.15250.56160.16320.50220.66050.21830.3961-0.12921.0815-0.0121-0.00730.81440.1080.3524355.2019506.0983772.0097
612.3236-3.92510.04148.9555-2.22718.0495-0.022-0.0642-0.09920.1427-0.4757-0.44240.44560.47030.27990.8123-0.1543-0.06010.52480.47160.575361.0067494.4384774.62
621.96831.1842-0.28532.2097-0.37271.33110.37620.3534-0.22730.1174-0.3808-0.4471-0.1532-0.185-0.04941.07170.3689-0.1750.83540.03960.2395331.0568484.3324779.0593
631.31810.07421.40731.93850.04572.08250.3375-0.05840.3629-0.25690.01390.6471-0.1029-1.0815-0.29180.67330.2463-0.08161.26960.08380.5742314.1889478.1815776.0911
643.29812.193-3.20993.1386-2.50323.20110.208-0.07140.04930.14940.080.5134-0.4296-0.1502-0.34350.72540.45780.04650.9110.09240.2826312.6755493.0302770.5808
652.24860.01770.86752.53390.66390.506-0.27180.08270.13760.4511-0.0264-0.0575-0.05880.10840.16880.88260.0677-0.68321.0025-0.23960.7883328.6758495.3323770.318
662.6283-1.56991.71831.9513-0.23671.740.70080.45860.2425-0.0848-0.11620.179-0.2652-0.6149-0.57851.07470.1555-0.46920.8712-0.18891.5735339.2087503.0393765.9146
673.2203-0.72192.11971.45322.07676.60310.16460.4978-0.5357-0.86010.0313-0.0358-0.64860.4588-0.45020.6786-0.0350.00720.9342-0.03920.1975322.2091473.6673779.219
680.0842-0.3469-0.0933.13390.0490.1711-0.2457-0.431-0.13330.8120.0177-0.2688-0.1606-0.48620.18110.7034-0.2133-0.02330.9115-0.06060.3438324.0455491.9458752.2517
691.1402-0.0215-0.06256.8867-4.80223.3525-0.07640.52240.25160.21160.36070.68360.0717-0.9265-0.23610.9180.0096-0.02681.04420.03120.3853326.138504.9621757.8087
703.7551-4.2783.55195.5455-5.18995.3067-0.3729-1.09140.6210.53660.5283-0.26260.1330.3196-0.0440.82740.3393-0.0331.0287-0.11630.4663318.2482500.4442751.3243
716.67370.14871.76935.04811.09772.0002-0.29370.38040.3534-0.4242-0.03780.6715-0.7502-0.83390.28781.2411-0.034-0.36661.3322-0.0530.3333316.0051495.7823748.9233
725.3583-1.79024.05986.6106-0.57895.8873-0.2672-0.36320.2870.37110.2974-0.69950.63291.7183-0.10760.74660.1474-0.13170.90450.10650.4374322.2871483.1892763.4192
730.8668-0.22970.01050.1850.02750.9499-0.1043-0.07940.050.12550.1013-0.02460.07880.17390.16750.7257-0.0204-0.08370.6681-0.0982-0.0418328.4821483.5146749.7956
743.3734-0.5698-0.3670.3255-0.25190.46420.0501-0.9395-0.33140.050.0576-0.01440.1518-0.08760.00481.1918-0.0809-0.14670.70910.1250.2438326.4181474.8564753.4373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 105 through 126 )
2X-RAY DIFFRACTION2chain 'H' and (resid 127 through 151 )
3X-RAY DIFFRACTION3chain 'H' and (resid 152 through 166 )
4X-RAY DIFFRACTION4chain 'I' and (resid 61 through 92 )
5X-RAY DIFFRACTION5chain 'I' and (resid 93 through 131 )
6X-RAY DIFFRACTION6chain 'I' and (resid 132 through 155 )
7X-RAY DIFFRACTION7chain 'I' and (resid 156 through 342 )
8X-RAY DIFFRACTION8chain 'I' and (resid 343 through 393 )
9X-RAY DIFFRACTION9chain 'I' and (resid 394 through 430 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 48 )
11X-RAY DIFFRACTION11chain 'J' and (resid 49 through 64 )
12X-RAY DIFFRACTION12chain 'J' and (resid 65 through 137 )
13X-RAY DIFFRACTION13chain 'J' and (resid 138 through 166 )
14X-RAY DIFFRACTION14chain 'K' and (resid 60 through 92 )
15X-RAY DIFFRACTION15chain 'K' and (resid 93 through 154 )
16X-RAY DIFFRACTION16chain 'K' and (resid 155 through 260 )
17X-RAY DIFFRACTION17chain 'K' and (resid 261 through 430 )
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 57 )
19X-RAY DIFFRACTION19chain 'L' and (resid 58 through 126 )
20X-RAY DIFFRACTION20chain 'L' and (resid 127 through 166 )
21X-RAY DIFFRACTION21chain 'A' and (resid 61 through 92 )
22X-RAY DIFFRACTION22chain 'A' and (resid 93 through 156 )
23X-RAY DIFFRACTION23chain 'A' and (resid 157 through 237 )
24X-RAY DIFFRACTION24chain 'A' and (resid 238 through 284 )
25X-RAY DIFFRACTION25chain 'A' and (resid 285 through 342 )
26X-RAY DIFFRACTION26chain 'A' and (resid 343 through 430 )
27X-RAY DIFFRACTION27chain 'B' and (resid 1 through 23 )
28X-RAY DIFFRACTION28chain 'B' and (resid 24 through 37 )
29X-RAY DIFFRACTION29chain 'B' and (resid 38 through 57 )
30X-RAY DIFFRACTION30chain 'B' and (resid 58 through 74 )
31X-RAY DIFFRACTION31chain 'B' and (resid 75 through 86 )
32X-RAY DIFFRACTION32chain 'B' and (resid 87 through 104 )
33X-RAY DIFFRACTION33chain 'B' and (resid 105 through 137 )
34X-RAY DIFFRACTION34chain 'B' and (resid 138 through 151 )
35X-RAY DIFFRACTION35chain 'B' and (resid 152 through 166 )
36X-RAY DIFFRACTION36chain 'C' and (resid 62 through 115 )
37X-RAY DIFFRACTION37chain 'C' and (resid 116 through 155 )
38X-RAY DIFFRACTION38chain 'C' and (resid 156 through 284 )
39X-RAY DIFFRACTION39chain 'C' and (resid 285 through 393 )
40X-RAY DIFFRACTION40chain 'C' and (resid 394 through 430 )
41X-RAY DIFFRACTION41chain 'D' and (resid 1 through 23 )
42X-RAY DIFFRACTION42chain 'D' and (resid 24 through 74 )
43X-RAY DIFFRACTION43chain 'D' and (resid 75 through 86 )
44X-RAY DIFFRACTION44chain 'D' and (resid 87 through 104 )
45X-RAY DIFFRACTION45chain 'D' and (resid 105 through 116 )
46X-RAY DIFFRACTION46chain 'D' and (resid 117 through 151 )
47X-RAY DIFFRACTION47chain 'D' and (resid 152 through 166 )
48X-RAY DIFFRACTION48chain 'E' and (resid 62 through 94 )
49X-RAY DIFFRACTION49chain 'E' and (resid 95 through 156 )
50X-RAY DIFFRACTION50chain 'E' and (resid 157 through 259 )
51X-RAY DIFFRACTION51chain 'E' and (resid 260 through 342 )
52X-RAY DIFFRACTION52chain 'E' and (resid 343 through 394 )
53X-RAY DIFFRACTION53chain 'E' and (resid 395 through 430 )
54X-RAY DIFFRACTION54chain 'F' and (resid 1 through 46 )
55X-RAY DIFFRACTION55chain 'F' and (resid 47 through 74 )
56X-RAY DIFFRACTION56chain 'F' and (resid 75 through 116 )
57X-RAY DIFFRACTION57chain 'F' and (resid 117 through 137 )
58X-RAY DIFFRACTION58chain 'F' and (resid 138 through 151 )
59X-RAY DIFFRACTION59chain 'F' and (resid 152 through 166 )
60X-RAY DIFFRACTION60chain 'G' and (resid 61 through 131 )
61X-RAY DIFFRACTION61chain 'G' and (resid 132 through 155 )
62X-RAY DIFFRACTION62chain 'G' and (resid 156 through 237 )
63X-RAY DIFFRACTION63chain 'G' and (resid 238 through 313 )
64X-RAY DIFFRACTION64chain 'G' and (resid 314 through 342 )
65X-RAY DIFFRACTION65chain 'G' and (resid 343 through 364 )
66X-RAY DIFFRACTION66chain 'G' and (resid 365 through 393 )
67X-RAY DIFFRACTION67chain 'G' and (resid 394 through 430 )
68X-RAY DIFFRACTION68chain 'H' and (resid 1 through 23 )
69X-RAY DIFFRACTION69chain 'H' and (resid 24 through 37 )
70X-RAY DIFFRACTION70chain 'H' and (resid 38 through 46 )
71X-RAY DIFFRACTION71chain 'H' and (resid 47 through 57 )
72X-RAY DIFFRACTION72chain 'H' and (resid 58 through 74 )
73X-RAY DIFFRACTION73chain 'H' and (resid 75 through 86 )
74X-RAY DIFFRACTION74chain 'H' and (resid 87 through 104 )

+
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