[English] 日本語
Yorodumi
- PDB-7tz2: Structure of human Fibrinogen-like protein 1 -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of T cell activation / fibrinogen complex / regulation of immune response / collagen-containing extracellular matrix / adaptive immune response / signaling receptor binding / extracellular space / extracellular region
Similarity search - Function
Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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