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- PDB-4iua: Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepat... -

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Basic information

Entry
Database: PDB / ID: 4iua
TitleCrystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor
ComponentsHepatocyte growth factor
KeywordsHORMONE / HGF/SF / KRINGLE domain / GROWTH FACTOR
Function / homology
Function and homology information


positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 ...positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 / MET receptor recycling / Negative regulation of MET activity / RAF/MAP kinase cascade / regulation of p38MAPK cascade / positive regulation of myelination / PIP3 activates AKT signaling / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Platelet degranulation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / hepatocyte growth factor receptor signaling pathway / myoblast proliferation / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of peptidyl-serine phosphorylation / cell chemotaxis / liver development / epithelial cell proliferation / growth factor activity / cell morphogenesis / negative regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / protein-containing complex binding / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 3-Layer(bba) Sandwich / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsTolbert, W.D. / Zhou, E. / Kovach, A. / Melcher, K. / Xu, H.E.
CitationJournal: To be Published
Title: Crystal Structure of the NK2 Fragment of the mouse Hepatocyte Growth Factor/Scatter Factor
Authors: Tolbert, W.D. / Zhou, E. / Kovach, A. / Melcher, K. / Xu, H.E.
History
DepositionJan 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatocyte growth factor
B: Hepatocyte growth factor
C: Hepatocyte growth factor
D: Hepatocyte growth factor
E: Hepatocyte growth factor
F: Hepatocyte growth factor
G: Hepatocyte growth factor
H: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,13933
Polymers243,3158
Non-polymers3,82425
Water0
1
A: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8454
Polymers30,4141
Non-polymers4303
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1796
Polymers30,4141
Non-polymers7655
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9874
Polymers30,4141
Non-polymers5733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9415
Polymers30,4141
Non-polymers5264
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6532
Polymers30,4141
Non-polymers2381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9415
Polymers30,4141
Non-polymers5264
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8454
Polymers30,4141
Non-polymers4303
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7493
Polymers30,4141
Non-polymers3342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Hepatocyte growth factor
F: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7869
Polymers60,8292
Non-polymers9577
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-77 kcal/mol
Surface area25180 Å2
MethodPISA
10
B: Hepatocyte growth factor
C: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,16610
Polymers60,8292
Non-polymers1,3378
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-69 kcal/mol
Surface area25720 Å2
MethodPISA
11
D: Hepatocyte growth factor
H: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6908
Polymers60,8292
Non-polymers8616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-68 kcal/mol
Surface area24430 Å2
MethodPISA
12
E: Hepatocyte growth factor
G: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4976
Polymers60,8292
Non-polymers6694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-44 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.620, 127.328, 129.600
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hepatocyte growth factor / / Hepatopoietin-A / Scatter factor / SF / Hepatocyte growth factor alpha chain / Hepatocyte growth ...Hepatopoietin-A / Scatter factor / SF / Hepatocyte growth factor alpha chain / Hepatocyte growth factor beta chain


Mass: 30414.326 Da / Num. of mol.: 8 / Fragment: NK2 fragment (UNP residues 31-290) / Mutation: C215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hgf / Plasmid: PET-DUET1/MBP-TRX / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE) / References: UniProt: Q08048
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM ammonium sulfate, 18% PEG 4000, 200 mM HEPES pH 7.0, 5% 2-METHYL-2,4-PENTANEDIOL, 0.5 mM beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. all: 57781 / Num. obs: 57775 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.05-3.165.90.7062.257171100
3.16-3.295.90.5342.957521100
3.29-3.435.90.3714.557711100
3.43-3.625.90.2527.457401100
3.62-3.845.90.18310.757601100
3.84-4.145.80.13814.557721100
4.14-4.555.80.11416.457891100
4.55-5.215.80.09319.557781100
5.21-6.555.70.08220.958101100
6.55-305.40.06424.55886199.9

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
CNSrefinement
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HN4
Resolution: 3.05→29.775 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 5877 10.18 %RANDOM
Rwork0.1758 ---
obs0.1829 57732 99.5 %-
all-57781 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16403 0 225 0 16628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917160
X-RAY DIFFRACTIONf_angle_d1.26623075
X-RAY DIFFRACTIONf_dihedral_angle_d17.1286540
X-RAY DIFFRACTIONf_chiral_restr0.0862214
X-RAY DIFFRACTIONf_plane_restr0.0063002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.07250.34771650.28461497X-RAY DIFFRACTION86
3.0725-3.10860.34842150.26641665X-RAY DIFFRACTION100
3.1086-3.14650.34621960.26711759X-RAY DIFFRACTION100
3.1465-3.18630.35852180.26291745X-RAY DIFFRACTION100
3.1863-3.22810.32221950.25861684X-RAY DIFFRACTION100
3.2281-3.27230.34622010.25781727X-RAY DIFFRACTION100
3.2723-3.3190.36281830.25611754X-RAY DIFFRACTION100
3.319-3.36850.33461810.25741729X-RAY DIFFRACTION100
3.3685-3.4210.32572120.22421734X-RAY DIFFRACTION100
3.421-3.4770.28121840.2131715X-RAY DIFFRACTION100
3.477-3.53690.26561960.20191737X-RAY DIFFRACTION100
3.5369-3.60110.27781830.19121738X-RAY DIFFRACTION100
3.6011-3.67020.27811940.18311714X-RAY DIFFRACTION100
3.6702-3.7450.23912310.16981717X-RAY DIFFRACTION100
3.745-3.82630.23042060.16381731X-RAY DIFFRACTION100
3.8263-3.91510.241860.15761739X-RAY DIFFRACTION100
3.9151-4.01280.23241990.1531731X-RAY DIFFRACTION100
4.0128-4.1210.23282010.1621727X-RAY DIFFRACTION100
4.121-4.2420.24261870.16331759X-RAY DIFFRACTION100
4.242-4.37850.24061840.15451728X-RAY DIFFRACTION100
4.3785-4.53440.21041850.15281775X-RAY DIFFRACTION100
4.5344-4.71530.18212070.14461706X-RAY DIFFRACTION100
4.7153-4.9290.20711920.1431761X-RAY DIFFRACTION100
4.929-5.18760.20381980.14541740X-RAY DIFFRACTION100
5.1876-5.51070.21321830.14251761X-RAY DIFFRACTION100
5.5107-5.93310.19671970.13991722X-RAY DIFFRACTION100
5.9331-6.52450.22241760.15651776X-RAY DIFFRACTION100
6.5245-7.45560.26482170.16241729X-RAY DIFFRACTION100
7.4556-9.34480.21211980.1571783X-RAY DIFFRACTION100
9.3448-29.77630.22462070.191772X-RAY DIFFRACTION99
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)
10.63130.3928-0.00952.87452.03922.25110.0691-0.1824-0.08810.41090.302-0.59850.40470.531-0.25810.17690.1002-0.0680.31810.03970.3029120.6576.24222.8691
20.3233-0.01580.09711.95631.71552.77870.01690.30090.2813-0.2066-0.31810.4685-0.2225-0.54910.21340.1463-0.0258-0.05480.19490.06780.472179.14917.4309-7.8692
32.22270.2929-0.03843.62980.76431.54610.1482-0.01750.13610.558-0.25660.81230.0783-0.32050.10580.2558-0.04190.09620.14180.03420.310776.1327-9.4912-4.4128
41.7381-0.47131.01812.8771-0.8483.12090.09060.3367-0.0266-0.4668-0.2579-0.66530.32980.47570.11410.2690.00640.09550.38790.0440.3462135.065412.198657.0363
52.18310.17070.26581.1628-0.75823.87660.1695-0.3023-0.04780.14460.13750.32430.6889-1.0622-0.2410.4651-0.14340.01550.50590.06320.250290.815218.936540.8447
62.66110.1308-0.90552.05240.94624.02550.11850.22420.2111-0.13240.2062-0.4249-0.36250.9221-0.22130.2336-0.08570.03010.43080.0790.2317123.762310.3482-24.098
71.48151.34410.70841.7262-0.25291.9870.1037-0.47260.47810.26410.14930.51480.0877-0.841-0.21620.3659-0.06140.07620.95320.07950.393593.753922.899267.5726
82.51720.10740.24263.6845-1.03071.7389-0.0516-0.0490.40380.4011-0.1874-1.0078-0.06610.22440.22970.3479-0.0655-0.08170.3516-0.04450.5625137.754138.86161.557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 290 )
2X-RAY DIFFRACTION2chain 'B' and (resid 37 through 290 )
3X-RAY DIFFRACTION3chain 'C' and (resid 37 through 290 )
4X-RAY DIFFRACTION4chain 'D' and (resid 37 through 290 )
5X-RAY DIFFRACTION5chain 'E' and (resid 37 through 290 )
6X-RAY DIFFRACTION6chain 'F' and (resid 37 through 290 )
7X-RAY DIFFRACTION7chain 'G' and (resid 38 through 290 )
8X-RAY DIFFRACTION8chain 'H' and (resid 39 through 290 )

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