[English] 日本語
Yorodumi
- PDB-9d20: Crystal structure of DLK1 in complex with ACVR2B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d20
TitleCrystal structure of DLK1 in complex with ACVR2B
Components
  • Activin receptor type-2B
  • Protein delta homolog 1
KeywordsSIGNALING PROTEIN / DLK1 / ACVR2B / Complex / SIGNALING
Function / homology
Function and homology information


Regulation of signaling by NODAL / activin receptor activity / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / venous blood vessel development / lymphangiogenesis / trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex ...Regulation of signaling by NODAL / activin receptor activity / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / venous blood vessel development / lymphangiogenesis / trophoblast cell migration / retina vasculature development in camera-type eye / embryonic foregut morphogenesis / activin receptor complex / artery development / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transforming growth factor beta receptor activity, type II / transforming growth factor beta receptor activity, type III / activin binding / pattern specification process / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / Signaling by NODAL / gastrulation with mouth forming second / pancreas development / kinase activator activity / determination of left/right symmetry / negative regulation of ossification / insulin secretion / negative regulation of cold-induced thermogenesis / anterior/posterior pattern specification / skeletal system morphogenesis / cell surface receptor protein serine/threonine kinase signaling pathway / organ growth / growth factor binding / mesoderm development / odontogenesis of dentin-containing tooth / roof of mouth development / blood vessel remodeling / negative regulation of Notch signaling pathway / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / protein serine/threonine/tyrosine kinase activity / Activated NOTCH1 Transmits Signal to the Nucleus / post-embryonic development / kidney development / lung development / cellular response to growth factor stimulus / heart development / intracellular iron ion homeostasis / cell differentiation / receptor complex / protein serine/threonine kinase activity / calcium ion binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / extracellular space / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain ...: / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-L-fucopyranose / Protein delta homolog 1 / Activin receptor type-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.673 Å
AuthorsMing, Q. / Antfolk, D. / Luca, V.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133482 United States
CitationJournal: To Be Published
Title: Molecular mechanism of Activin receptor inhibition by Delta-like non-canonical Notch ligand 1
Authors: Antfolk, D. / Ming, Q. / Luca, V.C.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Activin receptor type-2B
D: Protein delta homolog 1
A: Activin receptor type-2B
B: Protein delta homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98021
Polymers39,6784
Non-polymers2,30217
Water21612
1
E: Activin receptor type-2B
D: Protein delta homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,10012
Polymers19,8392
Non-polymers1,26110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-31 kcal/mol
Surface area11150 Å2
MethodPISA
2
A: Activin receptor type-2B
B: Protein delta homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8809
Polymers19,8392
Non-polymers1,0417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-27 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.980, 52.970, 97.990
Angle α, β, γ (deg.)90.00, 118.99, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules EADB

#1: Protein Activin receptor type-2B / Activin receptor type IIB / ACTR-IIB


Mass: 11219.317 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACVR2B / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q13705, receptor protein serine/threonine kinase
#2: Protein Protein delta homolog 1 / DLK-1 / pG2


Mass: 8619.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLK1, DLK / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P80370

-
Sugars , 3 types, 8 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 21 molecules

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


Mass: 62.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.67→35.89 Å / Num. obs: 15578 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.059 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.67-2.770.65215500.860.7691
2.77-2.880.4515390.9080.5331
2.88-3.010.30315470.9580.3591
3.01-3.170.17915430.9850.2131
3.17-3.370.11315520.9930.1361
3.37-3.630.0715390.9960.0841
3.63-3.990.05215590.9970.0611
3.99-4.570.03915540.9990.0461
4.57-5.750.03515750.9980.0421
5.75-35.890.02916180.9990.0351

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.673→35.888 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 776 5.02 %
Rwork0.2124 --
obs0.2139 15468 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.673→35.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 139 12 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042841
X-RAY DIFFRACTIONf_angle_d0.7863866
X-RAY DIFFRACTIONf_dihedral_angle_d19.6011710
X-RAY DIFFRACTIONf_chiral_restr0.047422
X-RAY DIFFRACTIONf_plane_restr0.004499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6731-2.84060.40321260.36062388X-RAY DIFFRACTION97
2.8406-3.05980.38541270.312411X-RAY DIFFRACTION99
3.0598-3.36750.3651300.27752453X-RAY DIFFRACTION99
3.3675-3.85430.28331290.21072438X-RAY DIFFRACTION99
3.8543-4.85410.17841300.17572474X-RAY DIFFRACTION100
4.8541-35.80.20111340.19112528X-RAY DIFFRACTION99
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)
10.4451-0.6687-0.3810.1771-0.0524-0.20770.30450.17470.21840.0215-0.2038-0.6544-0.4222-0.39540.00020.6636-0.0746-0.01160.71260.00550.692464.41828.250520.3069
2-0.01170.32270.10310.52460.76120.3818-0.49730.1082-0.5158-0.18290.4142-0.34070.72160.1357-0.00120.5266-0.12190.04130.7294-0.01560.515552.891726.332520.6348
30.1077-0.0539-0.06730.1540.32650.0387-0.60050.0592-0.72760.1180.18420.12150.6035-0.0622-0.00010.7687-0.11730.10880.7793-0.02920.838149.327121.681419.4833
40.13040.0603-0.14140.08860.24120.1042-0.5563-0.06620.24140.42960.2931-0.3550.13020.4388-0.00030.7046-0.014-0.08540.84490.00050.56748.12138.202324.4648
51.2687-0.13420.54870.8872-0.46141.2138-0.55590.9126-0.49930.0455-0.08450.21730.7316-0.8977-1.79630.9535-0.07630.26290.906-0.09010.941536.5422.340135.1218
6-0.03610.0161-0.019-0.00780.00720.05131.3385-0.2255-0.9877-0.48660.31430.25930.29230.29990.03571.9445-0.6661-0.22761.31290.13941.410625.54888.909433.6143
70.09170.00640.03350.06170.00740.0461-0.024-0.41490.13070.47350.04810.5282-0.03780.3705-0.00010.64660.05940.0640.76990.08310.603639.37910.546515.7029
8-0.0177-0.0151-0.05020.11020.0852-0.09830.38680.54521.0267-0.73530.1177-0.5526-0.1806-0.4837-0.00040.6212-0.04270.20410.6137-0.09651.032548.772515.2946-0.4012
90.01270.2163-0.05240.0747-0.09180.00920.892-0.39990.4576-0.7227-0.1276-0.10250.42170.68510.00171.09320.12850.21140.7260.05420.958155.252712.284-13.1436
100.3261-0.3255-0.16730.201-0.5530.2099-0.6715-0.6474-0.31510.68280.9397-0.1385-0.29560.05470.03140.5648-0.01960.04040.6402-0.04590.634215.5187-0.324215.5938
111.1730.3254-0.31120.6664-0.29070.89340.0604-0.36040.18040.0236-0.24740.64650.0051-0.0047-0.00010.5597-0.04990.05780.5463-0.05780.805427.57262.517410.1813
120.78730.59910.37610.1560.34210.7208-0.05240.2082-0.30710.52830.20140.4922-0.1513-0.056300.72210.06320.10470.54490.00260.989727.8973-1.76724.6812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:55)
2X-RAY DIFFRACTION2(chain A and resid 56:86)
3X-RAY DIFFRACTION3(chain A and resid 87:118)
4X-RAY DIFFRACTION4(chain B and resid 172:198)
5X-RAY DIFFRACTION5(chain B and resid 199:232)
6X-RAY DIFFRACTION6(chain B and resid 233:248)
7X-RAY DIFFRACTION7(chain D and resid 173:214)
8X-RAY DIFFRACTION8(chain D and resid 215:234)
9X-RAY DIFFRACTION9(chain D and resid 235:251)
10X-RAY DIFFRACTION10(chain E and resid 25:48)
11X-RAY DIFFRACTION11(chain E and resid 49:93)
12X-RAY DIFFRACTION12(chain E and resid 94:118)

+
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