[English] 日本語
Yorodumi
- PDB-1frt: CRYSTAL STRUCTURE OF THE COMPLEX OF RAT NEONATAL FC RECEPTOR WITH FC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1frt
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF RAT NEONATAL FC RECEPTOR WITH FC
Components
  • BETA 2-MICROGLOBULIN
  • IGG FC
  • NEONATAL FC RECEPTOR
KeywordsCOMPLEX (RECEPTOR/IMMUNOGLOBULIN) / COMPLEX (RECEPTOR-IMMUNOGLOBULIN) / COMPLEX (RECEPTOR-IMMUNOGLOBULIN) complex
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway / IgG receptor activity / IgG binding / Neutrophil degranulation / regulation of membrane depolarization ...Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway / IgG receptor activity / IgG binding / Neutrophil degranulation / regulation of membrane depolarization / humoral immune response / beta-2-microglobulin binding / response to cadmium ion / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / protein refolding / cellular response to lipopolysaccharide / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / response to xenobiotic stimulus / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / : / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Beta-2-microglobulin / IgG receptor FcRn large subunit p51
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 4.5 Å
AuthorsBurmeister, W.P. / Bjorkman, P.J.
Citation
Journal: Nature / Year: 1994
Title: Crystal structure of the complex of rat neonatal Fc receptor with Fc.
Authors: Burmeister, W.P. / Huber, A.H. / Bjorkman, P.J.
#1: Journal: Nature / Year: 1994
Title: Crystal Structure at 2.2 Angstroms Resolution of the Mhc-Related Neonatal Fc Receptor
Authors: Burmeister, W.P. / Gastinel, L.N. / Simister, N.E. / Blum, M.L. / Bjorkman, P.J.
#2: Journal: Immunity / Year: 1994
Title: Investigation of the Interaction between the Class I Mhc-Related Fc Receptor and its Immunoglobulin G Ligand
Authors: Raghavan, M. / Chen, M.Y. / Gastinel, L.N. / Bjorkman, P.J.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Stoichiometry of Binding of a Complex between a Rat Intestinal Fc Receptor and Fc
Authors: Huber, A.H. / Kelly, R.F. / Gastinel, L.N. / Bjorkman, P.J.
#4: Journal: Biochemistry / Year: 1981
Title: Crystallographic Refinement and Atomic Models of a Human Fc Fragment and its Complex with Fragment B of Protein a from Staphylococcus Aureus at 2.9-And 2.8-Angstroms Resolution
Authors: Deisenhofer, J.
History
DepositionNov 11, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 5, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _pdbx_database_status.process_site ..._chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEONATAL FC RECEPTOR
B: BETA 2-MICROGLOBULIN
C: IGG FC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6126
Polymers65,3983
Non-polymers2,2143
Water00
1
A: NEONATAL FC RECEPTOR
B: BETA 2-MICROGLOBULIN
C: IGG FC
hetero molecules

A: NEONATAL FC RECEPTOR
B: BETA 2-MICROGLOBULIN
C: IGG FC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,22412
Polymers130,7956
Non-polymers4,4286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Unit cell
Length a, b, c (Å)125.000, 145.000, 216.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Atom site foot note1: CIS PROLINE - PRO A 207 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO C 374
DetailsMTRIX THE INFORMATION PRESENTED ON SYMMETRY RECORDS BELOW DESCRIBE TRANSFORMATIONS TO GENERATE CRYSTALLOGRAPHIC RELATIONSHIPS AS DESCRIBED IN THE STATEMENT THAT FOLLOWS EACH SYMMETRY OPERATOR. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD S1 C 1 - C 443 ? 1 - ? 443 THIS TRANSFORMATION GENERATES THE SECOND CHAIN OF THE FC MOLECULE. IF THE SAME OPERATION IS ALSO APPLIED TO THE FCRN MOLECULE, THE "STANDING UP" FCRNFC COMPLEX DISCUSSED IN THE ACCOMPANYING PAPER IS GENERATED. S2 A 1 - A 405 ? 1 - ? 405 S2 B 1 - B 99 ? 1 - ? 99 THIS TRANSFORMATION GENERATES THE SECOND SUBUNIT FOR THE "LYING DOWN" FC RECEPTOR DIMER PRESENTED IN THE ACCOMPANYING PAPER. SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 -1.000000 0.000000 145.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 108.25000 SYMMETRY1 2 -1.000000 0.000000 0.000000 250.00000 SYMMETRY2 2 0.000000 -1.000000 0.000000 72.50000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein NEONATAL FC RECEPTOR


Mass: 30322.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BETA-2-MICROGLOBULIN / Organ: SERUM (MIXTURE OF SEVERAL SUBTYPES) / Plasmid: PBJ5-GS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P13599
#2: Protein BETA 2-MICROGLOBULIN


Mass: 11652.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BETA-2-MICROGLOBULIN / Organ: SERUM (MIXTURE OF SEVERAL SUBTYPES) / Plasmid: PBJ5-GS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P07151
#3: Protein IGG FC


Mass: 23422.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: BETA-2-MICROGLOBULIN / Organ: SERUM (MIXTURE OF SEVERAL SUBTYPES) / Plasmid: PBJ5-GS / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: GenBank: 243866

-
Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-D-6-deoxy-Altp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY
Sequence detailsTHERE ARE A NUMBER OF CLOSE CONTACTS BETWEEN ATOMS IN THIS THIS MOLECULE AND IN SYMMETRY-RELATED MOLECULES.
Source detailsSOURCE 1 MOLECULE_NAME: FC (IGG) RECEPTOR, NEONATAL (FCRN) THE CELL LINE SECRETES A SOLUBLE FCRN ...SOURCE 1 MOLECULE_NAME: FC (IGG) RECEPTOR, NEONATAL (FCRN) THE CELL LINE SECRETES A SOLUBLE FCRN HETERODIMER COMPOSED OF THE EXTRACELLULAR DOMAINS OF THE RAT FCRN HEAVY CHAIN ASSOCIATED WITH RAT BETA-2-MICROGLOBULIN. SOURCE 2 MOLECULE_NAME: FC FRAGMENT (IGG) OBTAINED FROM JACKSON IMMUNORESEARCH LABS. THE FC FRAGMENT IS A MIXTURE OF SUBTYPES 1, 2A, 2B, AND 2C. THE N-TERMINUS IS NOT PRECISELY KNOWN, BUT THE CLEAVAGE SITE IS C-TERMINAL TO THE DISULFIDE BONDS OF THE HINGE REGION. THE FRAGMENT IS, THEREFORE, A NON-COVALENT DIMER.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
pH: 6.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mMPIPES1drop
30.05 %1dropNaN3
40.67 Msodium tartarate1reservoir
5100 mMcitrate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 8527 / % possible obs: 67 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 4.5 Å / Lowest resolution: 25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.125
Reflection shell
*PLUS
Highest resolution: 4.5 Å / Lowest resolution: 4.7 Å / % possible obs: 23 % / Rmerge(I) obs: 0.289

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 4.5→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.423 --
obs0.423 8433 67 %
Displacement parametersBiso mean: 199 Å2
Refinement stepCycle: LAST / Resolution: 4.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 148 0 4756

+
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://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