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- PDB-5aej: Crystal structure of human Gremlin-1 -

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Basic information

Entry
Database: PDB / ID: 5aej
TitleCrystal structure of human Gremlin-1
ComponentsGREMLIN-1
KeywordsSIGNALING PROTEIN / SIGNALING / GREMLIN / GROWTH FACTORS / INHIBITOR / CYSTINE KNOT / EXTRACELLULAR SIGNALLING / DAN FAMILY
Function / homology
Function and homology information


negative regulation of bone remodeling / sequestering of BMP from receptor via BMP binding / mesenchymal to epithelial transition involved in metanephros morphogenesis / negative regulation of monocyte chemotaxis / determination of dorsal identity / ureteric bud formation / negative regulation of osteoclast proliferation / morphogen activity / negative regulation of bone mineralization involved in bone maturation / BMP binding ...negative regulation of bone remodeling / sequestering of BMP from receptor via BMP binding / mesenchymal to epithelial transition involved in metanephros morphogenesis / negative regulation of monocyte chemotaxis / determination of dorsal identity / ureteric bud formation / negative regulation of osteoclast proliferation / morphogen activity / negative regulation of bone mineralization involved in bone maturation / BMP binding / Formation of the ureteric bud / negative regulation of bone trabecula formation / negative regulation of osteoblast proliferation / proximal/distal pattern formation / negative regulation of bone mineralization / cardiac muscle cell myoblast differentiation / regulation of epithelial to mesenchymal transition / positive regulation of branching involved in ureteric bud morphogenesis / cardiac muscle cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular endothelial growth factor signaling pathway / cell migration involved in sprouting angiogenesis / collagen fibril organization / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / limb development / positive regulation of cell migration involved in sprouting angiogenesis / regulation of focal adhesion assembly / negative regulation of SMAD protein signal transduction / positive regulation of receptor internalization / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / cytokine activity / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / positive regulation of angiogenesis / cell-cell signaling / : / receptor ligand activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Gremlin-1/2 / DAN / DAN domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsKisonaite, M. / Hyvonen, M.
CitationJournal: Biochem.J. / Year: 2016
Title: Structure of Gremlin-1 and Analysis of its Interaction with Bmp-2.
Authors: Kisonaite, M. / Wang, X. / Hyvonen, M.
History
DepositionAug 31, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GREMLIN-1
B: GREMLIN-1
C: GREMLIN-1
D: GREMLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3336
Polymers70,1414
Non-polymers1922
Water5,098283
1
C: GREMLIN-1
D: GREMLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1663
Polymers35,0702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-36.7 kcal/mol
Surface area14080 Å2
MethodPISA
2
A: GREMLIN-1
B: GREMLIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1663
Polymers35,0702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-36.1 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.816, 106.135, 78.521
Angle α, β, γ (deg.)90.00, 121.25, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4105, -0.5128, -0.754), (-0.5341, -0.5349, 0.6546), (-0.739, 0.6715, -0.05429)31.33, -43.47, 55.11
2given(-0.4079, 0.4903, 0.7702), (-0.5938, 0.4983, -0.6317), (-0.6935, -0.715, 0.08792)-95.87, 16.1, 81.36
3given(0.9976, 0.06277, -0.02763), (0.06261, -0.998, -0.006704), (-0.02799, 0.004958, -0.9996)0.2155, 51.33, 133.6

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Components

#1: Protein
GREMLIN-1 / CELL PROLIFERATION-INDUCING GENE 2 PROTEIN / CYSTEINE KNOT SUPERFAMILY 1 / BMP ANTAGONIST 1 / DAN ...CELL PROLIFERATION-INDUCING GENE 2 PROTEIN / CYSTEINE KNOT SUPERFAMILY 1 / BMP ANTAGONIST 1 / DAN DOMAIN FAMILY MEMBER 2 / DOWN-REGULATED IN MOS-TRANSFORMED CELLS PROTEIN / INCREASED IN HIGH GLUCOSE PROTEIN 2 / IHG-2


Mass: 17535.152 Da / Num. of mol.: 4 / Fragment: CYSTINE-KNOT DOMAIN, RESIDUES 72-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PUBS520 / References: UniProt: O60565
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCONTAINS N-TERMINAL HIS-TAG WITH TEV CLEAVAGE SITE

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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: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE
Crystal growpH: 4.5
Details: 2.1 M NACL, 0.1 M NA ACETATE, 0.3 M LI SULFATE, PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.9→41.63 Å / Num. obs: 47349 / % possible obs: 99.7 % / Observed criterion σ(I): 2.2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JPH

4jph


Resolution: 1.904→41.631 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 2306 4.9 %
Rwork0.1792 --
obs0.1806 47342 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→41.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 10 283 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073818
X-RAY DIFFRACTIONf_angle_d1.0385132
X-RAY DIFFRACTIONf_dihedral_angle_d20.8842442
X-RAY DIFFRACTIONf_chiral_restr0.066554
X-RAY DIFFRACTIONf_plane_restr0.007649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.904-1.94540.34221420.32812779X-RAY DIFFRACTION100
1.9454-1.99070.30311410.28542804X-RAY DIFFRACTION100
1.9907-2.04050.28691300.24742838X-RAY DIFFRACTION100
2.0405-2.09560.22441440.21382802X-RAY DIFFRACTION100
2.0956-2.15730.21831450.20622812X-RAY DIFFRACTION100
2.1573-2.22690.25241510.19912808X-RAY DIFFRACTION100
2.2269-2.30650.24051550.20062821X-RAY DIFFRACTION100
2.3065-2.39880.25441310.1922835X-RAY DIFFRACTION100
2.3988-2.5080.23431590.19262781X-RAY DIFFRACTION100
2.508-2.64020.25241460.19422833X-RAY DIFFRACTION100
2.6402-2.80560.26751360.18992842X-RAY DIFFRACTION100
2.8056-3.02220.19051320.17292817X-RAY DIFFRACTION100
3.0222-3.32620.20581290.17162836X-RAY DIFFRACTION100
3.3262-3.80720.17491640.15862803X-RAY DIFFRACTION99
3.8072-4.79550.1541470.13892808X-RAY DIFFRACTION99
4.7955-41.64050.19741540.16532817X-RAY DIFFRACTION98
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)
10.02580.03170.00760.675-0.89770.9985-0.0113-0.02340.03170.01710.14660.1016-0.07770.00230.02540.2019-0.00570.03420.20370.03040.2139-29.377823.832576.1584
20.1733-0.11610.06490.8483-0.38581.42480.0649-0.0366-0.13170.1576-0.0974-0.31630.01840.1786-0.00140.17460.03520.01380.23150.03670.2533-26.53039.08288.7014
30.3349-0.41270.24631.0781-0.92191.6468-0.01610.07260.208-0.1769-0.0731-0.2951-0.0140.25480.01270.1545-0.0327-0.02410.24780.05630.2672-28.13140.558345.7802
40.3528-0.16110.25580.5879-0.77080.6613-0.05060.0318-0.0650.03270.15390.14060.07060.01730.01730.23530.0127-0.01120.19710.02330.1814-29.617625.30258.4194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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