[English] 日本語
Yorodumi
- PDB-1m4u: Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m4u
TitleCrystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin
Components
  • Bone Morphogenetic Protein-7
  • Noggin
KeywordsHORMONE/GROWTH FACTOR / NOGGIN / BMP ANTAGONIST / BMP-7 / BONE MORPHOGENETIC PROTEIN / CYSTINE KNOT / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / notochord morphogenesis / negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / neural plate morphogenesis / positive regulation of hyaluranon cable assembly ...neural plate anterior/posterior regionalization / negative regulation of cardiac epithelial to mesenchymal transition / notochord morphogenesis / negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / neural plate morphogenesis / positive regulation of hyaluranon cable assembly / cell differentiation in hindbrain / negative regulation of cytokine activity / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / atrial cardiac muscle tissue morphogenesis / regulation of fibroblast growth factor receptor signaling pathway / ureteric bud formation / negative regulation of striated muscle cell apoptotic process / positive regulation of glomerulus development / embryonic skeletal joint morphogenesis / neural fold elevation formation / prostatic bud formation / ameloblast differentiation / nodal signaling pathway / positive regulation of epithelial cell differentiation / metanephric mesenchymal cell proliferation involved in metanephros development / embryonic camera-type eye morphogenesis / mesenchyme development / pharyngeal arch artery morphogenesis / endoderm formation / short-term synaptic potentiation / monocyte aggregation / ventricular compact myocardium morphogenesis / pituitary gland development / allantois development / mesonephros development / membranous septum morphogenesis / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / negative regulation of cartilage development / somite development / regulation of removal of superoxide radicals / hindbrain development / mesenchymal cell differentiation / BMP receptor binding / pericardium morphogenesis / cranial skeletal system development / positive regulation of branching involved in ureteric bud morphogenesis / endocardial cushion formation / negative regulation of SMAD protein signal transduction / pharyngeal system development / heart trabecula morphogenesis / Signaling by BMP / cellular response to BMP stimulus / embryonic pattern specification / branching involved in salivary gland morphogenesis / axial mesoderm development / regulation of phosphorylation / response to vitamin D / metanephros development / negative regulation of mitotic nuclear division / dorsal/ventral pattern formation / cardiac muscle tissue development / negative regulation of non-canonical NF-kappaB signal transduction / motor neuron axon guidance / positive regulation of heterotypic cell-cell adhesion / cartilage development / middle ear morphogenesis / positive regulation of dendrite development / face morphogenesis / embryonic limb morphogenesis / limb development / Molecules associated with elastic fibres / negative regulation of BMP signaling pathway / exploration behavior / ureteric bud development / embryonic digit morphogenesis / negative regulation of NF-kappaB transcription factor activity / smoothened signaling pathway / regulation of branching involved in prostate gland morphogenesis / negative regulation of osteoblast differentiation / branching morphogenesis of an epithelial tube / ventricular septum morphogenesis / spinal cord development / BMP signaling pathway / negative regulation of Notch signaling pathway / lung morphogenesis / cardiac septum morphogenesis / Formation of paraxial mesoderm / dendrite development / outflow tract morphogenesis / odontogenesis of dentin-containing tooth / regulation of neuronal synaptic plasticity / cytokine binding / somatic stem cell population maintenance / positive regulation of SMAD protein signal transduction / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of astrocyte differentiation / negative regulation of apoptotic signaling pathway
Similarity search - Function
Helix hairpin bin / Noggin / Noggin / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal ...Helix hairpin bin / Noggin / Noggin / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Bone morphogenetic protein 7 / Noggin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å
AuthorsGroppe, J. / Greenwald, J. / Wiater, E. / Rodriguez-Leon, J. / Economides, A.N. / Kwiatkowski, W. / Affolter, M. / Vale, W.W. / Izpisua-Belmonte, J.C. / Choe, S.
Citation
Journal: Nature / Year: 2002
Title: Structural Basis of BMP Signalling Inhibition by the Cystine Knot Protein Noggin
Authors: Groppe, J. / Greenwald, J. / Wiater, E. / Rodriguez-Leon, J. / Economides, A.N. / Kwiatkowski, W. / Affolter, M. / Vale, W.W. / Izpisua-Belmonte, J.C. / Choe, S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Three-dimensional structure of recombinant human osteogenic protein 1: Structural paradigm for the transforming growth factor beta superfamily
Authors: Griffith, D.L. / Keck, P.C. / Sampath, T.K. / Rueger, D.C. / Carlson, W.D.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
L: Bone Morphogenetic Protein-7
A: Noggin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3373
Polymers38,9132
Non-polymers4241
Water82946
1
L: Bone Morphogenetic Protein-7
A: Noggin
hetero molecules

L: Bone Morphogenetic Protein-7
A: Noggin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6746
Polymers77,8254
Non-polymers8492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area12100 Å2
ΔGint-63 kcal/mol
Surface area34570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.834, 99.834, 150.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: -y,-x,-z+.5

-
Components

#1: Protein Bone Morphogenetic Protein-7 / BMP-7 / Osteogenic protein 1 / OP-1


Mass: 15699.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DHFR- / Gene: BMP7 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18075
#2: Protein Noggin


Mass: 23212.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: high copy number derivative of pBR322 with a lacUV5 promoter
Gene: NOG / Plasmid: pRG301 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 lacIq / References: UniProt: Q13253
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.6 M disodium, 1.0 M monopotassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.6 Mdisodium1reservoir
31.0 Mmonopotassium phosphate1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.04888, 0.91987, 0.91957, 0.88557
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2001
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.048881
20.919871
30.919571
40.885571
ReflectionResolution: 2.42→60 Å / Num. all: 29713 / Num. obs: 28463 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.054
Reflection shellResolution: 2.42→2.483 Å / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 60 Å / Num. measured all: 92080 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Lowest resolution: 2.48 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.331

-
Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
REFMAC5refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.42→60.05 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.409 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27303 1441 5.1 %RANDOM
Rwork0.24078 ---
obs0.24243 27000 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.42→60.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 28 46 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0212590
X-RAY DIFFRACTIONr_bond_other_d0.0020.022288
X-RAY DIFFRACTIONr_angle_refined_deg3.0341.973515
X-RAY DIFFRACTIONr_angle_other_deg1.34535346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1733308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.63215476
X-RAY DIFFRACTIONr_chiral_restr0.2010.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022820
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02520
X-RAY DIFFRACTIONr_nbd_refined0.280.3637
X-RAY DIFFRACTIONr_nbd_other0.2820.32444
X-RAY DIFFRACTIONr_nbtor_other0.3430.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.5174
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2260.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.372
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.3187
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.513
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0620.51
X-RAY DIFFRACTIONr_mcbond_it1.781.51557
X-RAY DIFFRACTIONr_mcangle_it3.22722515
X-RAY DIFFRACTIONr_scbond_it4.11631033
X-RAY DIFFRACTIONr_scangle_it6.6024.51000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 120
Rwork0.287 2026
Refinement
*PLUS
Lowest resolution: 60 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.035
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3

+
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