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- PDB-7tz2: Structure of human Fibrinogen-like protein 1 -

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Basic information

Entry
Database: PDB / ID: 7tz2
TitleStructure of human Fibrinogen-like protein 1
ComponentsFibrinogen-like protein 1
KeywordsIMMUNOSUPPRESSANT / Immune suppression / Fibrinogen-like domain / Secretion / Oligomerization
Function / homology
Function and homology information


hepatocyte proliferation / fibrinogen complex / negative regulation of T cell activation / regulation of immune response / cell-matrix adhesion / platelet aggregation / collagen-containing extracellular matrix / adaptive immune response / signaling receptor binding / 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: 2.55 Å
AuthorsMing, Q. / Tran, T.H. / Luca, V.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133482 United States
V Foundation for Cancer Research United States
Rita Allen Foundation United States
CitationJournal: Nat.Immunol. / Year: 2022
Title: LAG3 ectodomain structure reveals functional interfaces for ligand and antibody recognition.
Authors: Ming, Q. / Celias, D.P. / Wu, C. / Cole, A.R. / Singh, S. / Mason, C. / Dong, S. / Tran, T.H. / Amarasinghe, G.K. / Ruffell, B. / Luca, V.C.
History
DepositionFeb 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 13, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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

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Assembly

Deposited unit
A: Fibrinogen-like protein 1
B: Fibrinogen-like protein 1
C: Fibrinogen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9644
Polymers81,9233
Non-polymers401
Water2,324129
1
A: Fibrinogen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3482
Polymers27,3081
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibrinogen-like protein 1


Theoretical massNumber of molelcules
Total (without water)27,3081
Polymers27,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fibrinogen-like protein 1


Theoretical massNumber of molelcules
Total (without water)27,3081
Polymers27,3081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.277, 110.893, 148.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 76 through 228 or (resid 229...
21(chain B and (resid 76 through 217 or resid 228...
31(chain C and (resid 76 through 217 or resid 228...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 76 through 228 or (resid 229...A76 - 228
121(chain A and (resid 76 through 228 or (resid 229...A229
131(chain A and (resid 76 through 228 or (resid 229...A76 - 541
141(chain A and (resid 76 through 228 or (resid 229...A76 - 541
151(chain A and (resid 76 through 228 or (resid 229...A76 - 541
161(chain A and (resid 76 through 228 or (resid 229...A76 - 541
211(chain B and (resid 76 through 217 or resid 228...B76 - 217
221(chain B and (resid 76 through 217 or resid 228...B228 - 261
231(chain B and (resid 76 through 217 or resid 228...B262
241(chain B and (resid 76 through 217 or resid 228...B75 - 545
251(chain B and (resid 76 through 217 or resid 228...B75 - 545
261(chain B and (resid 76 through 217 or resid 228...B75 - 545
271(chain B and (resid 76 through 217 or resid 228...B75 - 545
311(chain C and (resid 76 through 217 or resid 228...C76 - 217
321(chain C and (resid 76 through 217 or resid 228...C228
331(chain C and (resid 76 through 217 or resid 228...C229
341(chain C and (resid 76 through 217 or resid 228...C76 - 559
351(chain C and (resid 76 through 217 or resid 228...C76 - 559
361(chain C and (resid 76 through 217 or resid 228...C243
371(chain C and (resid 76 through 217 or resid 228...C76 - 559
381(chain C and (resid 76 through 217 or resid 228...C76 - 559
391(chain C and (resid 76 through 217 or resid 228...C76 - 559
3101(chain C and (resid 76 through 217 or resid 228...C76 - 559
3111(chain C and (resid 76 through 217 or resid 228...C76 - 559

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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: 27307.828 Da / Num. of mol.: 3 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGL1, HFREP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08830
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 M lithium chloride, 0.1 M citric acid pH 5.0 and 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 25222 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.92 Å2 / Rmerge(I) obs: 0.349 / Rpim(I) all: 0.157 / Rrim(I) all: 0.384 / Χ2: 1.576 / Net I/σ(I): 3 / Num. measured all: 144191
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.644.51.34724570.4210.6861.5180.55299.4
2.64-2.755.11.26624430.4620.6151.4130.56699.8
2.75-2.875.21.01724990.4940.4861.1310.63999.7
2.87-3.026.10.88824930.7230.3860.970.67999.8
3.02-3.216.10.64724810.8380.2810.7060.76699.8
3.21-3.465.80.40525200.9110.1830.4461.047100
3.46-3.816.20.29325130.9450.1260.3191.3299.7
3.81-4.366.20.20525150.9670.0880.2231.58899.9
4.36-5.4960.16425780.9730.0720.181.75499.7
5.49-505.70.1827230.9010.0830.1996.1299.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M7F

4m7f


Resolution: 2.55→45.3 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 1285 5.11 %
Rwork0.1846 23842 -
obs0.1871 25127 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.47 Å2 / Biso mean: 39.342 Å2 / Biso min: 20.71 Å2
Refinement stepCycle: final / Resolution: 2.55→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 1 129 5755
Biso mean--68.8 32.59 -
Num. residues----682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1989X-RAY DIFFRACTION16.998TORSIONAL
12B1989X-RAY DIFFRACTION16.998TORSIONAL
13C1989X-RAY DIFFRACTION16.998TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.650.36381160.27422584270098
2.65-2.770.31781350.23992570270599
2.77-2.920.28071560.226626152771100
2.92-3.10.30441620.231625802742100
3.1-3.340.27881220.204126692791100
3.34-3.680.23511490.162126282777100
3.68-4.210.19251490.149226702819100
4.21-5.30.15811620.133426912853100
5.3-45.30.21171340.19172835296999
Refinement TLS params.Method: refined / Origin x: 9.7811 Å / Origin y: -27.2764 Å / Origin z: 8.087 Å
111213212223313233
T0.3044 Å2-0.0089 Å20.012 Å2-0.2803 Å20.0014 Å2--0.2615 Å2
L-0.1037 °2-0.1027 °20.0688 °2-0.0657 °20.0274 °2--0.2954 °2
S-0.0053 Å °-0.0214 Å °0.023 Å °-0.0632 Å °-0.0015 Å °0.0338 Å °-0.0525 Å °0.0219 Å °-0.0437 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA76 - 541
2X-RAY DIFFRACTION1allB75 - 545
3X-RAY DIFFRACTION1allC76 - 559

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