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- PDB-9c6t: Structure of the Human ISM1 TSR-AMOP domains -

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Basic information

Entry
Database: PDB / ID: 9c6t
TitleStructure of the Human ISM1 TSR-AMOP domains
ComponentsIsthmin-1
KeywordsUNKNOWN FUNCTION / throspondin repeat domain / AMOP domain / adipokine
Function / homology
Function and homology information


negative regulation of angiogenesis / extracellular region
Similarity search - Function
AMOP domain / : / AMOP domain / AMOP domain profile. / Adhesion-associated domain present in MUC4 and other proteins / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
alpha-D-mannopyranose / Isthmin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsStayrook, S. / Li, T. / Klein, D.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling.
Authors: Li, T. / Stayrook, S.E. / Li, W. / Wang, Y. / Li, H. / Zhang, J. / Liu, Y. / Klein, D.E.
History
DepositionJun 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isthmin-1
B: Isthmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8406
Polymers56,1192
Non-polymers7214
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-9 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.255, 114.255, 168.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Isthmin-1


Mass: 28059.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISM1, C20orf82, ISM / Production host: Homo sapiens (human) / References: UniProt: B1AKI9
#2: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 4.5 Å3/Da / Density % sol: 72.85 % / Description: hexagonal
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M NaMelonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.41→49.47 Å / Num. obs: 17232 / % possible obs: 96.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 197.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Rrim(I) all: 0.073 / Net I/σ(I): 9.3 / Num. measured all: 89619 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.41-3.685.33.4171874635540.3811.4643.7360.397.8
9.02-49.474.80.02545629530.9990.0120.02847.389.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.41→49.47 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3659 867 5.04 %
Rwork0.3316 --
obs0.3334 17187 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.41→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 44 0 3622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043701
X-RAY DIFFRACTIONf_angle_d0.7345000
X-RAY DIFFRACTIONf_dihedral_angle_d18.842535
X-RAY DIFFRACTIONf_chiral_restr0.04538
X-RAY DIFFRACTIONf_plane_restr0.008637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-3.620.41171320.36722711X-RAY DIFFRACTION98
3.62-3.90.44551470.39472758X-RAY DIFFRACTION98
3.9-4.30.40191340.35742707X-RAY DIFFRACTION97
4.3-4.920.42041340.33342712X-RAY DIFFRACTION97
4.92-6.190.31151690.29812716X-RAY DIFFRACTION96
6.19-49.470.27761510.26012716X-RAY DIFFRACTION92
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)
10.0282-0.0285-0.01890.031-0.040.0092-0.05040.0738-0.11660.0563-0.0312-0.22180.0563-0.16510.0019-0.14470.3871-0.2213-0.33740.32570.2323-63.3716.319822.4413
20.0491-0.05290.04780.1373-0.03690.02460.26730.10270.08590.22390.1821-0.2842-0.10990.02780.57460.16081.13380.00320.0520.60240.0753-71.033543.952311.771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 222:464)
2X-RAY DIFFRACTION2(chain B and resseq 222:463)

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