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- PDB-9q35: Fibrinogen domain dimer from human Fibrinogen-like protein 1 (FGL-1) -

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Basic information

Entry
Database: PDB / ID: 9q35
TitleFibrinogen domain dimer from human Fibrinogen-like protein 1 (FGL-1)
ComponentsFibrinogen-like protein 1
KeywordsIMMUNOSUPPRESSANT / fibrinogen-like domain / disulfide-stabilized dimer / immune checkpoint ligand / regulation of immune response
Function / homology
Function and homology information


hepatocyte proliferation / fibrinogen complex / negative regulation of T cell activation / regulation of immune response / blood coagulation / : / adaptive immune response / extracellular space / extracellular region
Similarity search - Function
Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Fibrinogen-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsNyovanie, S. / Patskovsky, Y. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243486-01A1 United States
CitationJournal: To Be Published
Title: Fibrinogen domain dimer from human Fibrinogen-like protein 1 (FGL-1)
Authors: Nyovanie, S. / Patskovsky, Y. / Krogsgaard, M.
History
DepositionAug 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrinogen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9766
Polymers28,6651
Non-polymers3105
Water4,288238
1
A: Fibrinogen-like protein 1
hetero molecules

A: Fibrinogen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,95212
Polymers57,3312
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3970 Å2
ΔGint16 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.012, 39.777, 65.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Fibrinogen-like protein 1 / HP-041 / Hepassocin / HPS / Hepatocyte-derived fibrinogen-related protein 1 / HFREP-1 / Liver ...HP-041 / Hepassocin / HPS / Hepatocyte-derived fibrinogen-related protein 1 / HFREP-1 / Liver fibrinogen-related protein 1 / LFIRE-1


Mass: 28665.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGL1, HFREP1 / Plasmid: PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08830
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10% PEG8000, 8% ETHYLENE GLYCOL, 0.1 M HEPES, PH 7.5
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 9, 2021 / Details: SI 111 CRYSTAL
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.74→37.14 Å / Num. obs: 24297 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.094 / Χ2: 0 / Net I/σ(I): 9.6
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1034 / Χ2: 0 / % possible all: 78.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACT4.3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FZD

1fzd


Resolution: 1.74→37.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.202 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21498 684 2.8 %RANDOM
Rwork0.16553 ---
obs0.16691 23578 97.57 %-
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: 30.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.74→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 20 238 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0122097
X-RAY DIFFRACTIONr_bond_other_d00.0161831
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.8092846
X-RAY DIFFRACTIONr_angle_other_deg0.5971.7924225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.055511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29710338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1613.064973
X-RAY DIFFRACTIONr_mcbond_other3.1353.064973
X-RAY DIFFRACTIONr_mcangle_it4.4845.4651223
X-RAY DIFFRACTIONr_mcangle_other4.4825.4731224
X-RAY DIFFRACTIONr_scbond_it4.0283.4631124
X-RAY DIFFRACTIONr_scbond_other4.0263.4631125
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0766.1531612
X-RAY DIFFRACTIONr_long_range_B_refined8.02533.532456
X-RAY DIFFRACTIONr_long_range_B_other7.92531.942387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.742→1.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 38 -
Rwork0.303 1386 -
obs--80.18 %

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