[English] 日本語
Yorodumi
- PDB-3i85: The Crystal Structure of Human EMMPRIN N-terminal Domain 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i85
TitleThe Crystal Structure of Human EMMPRIN N-terminal Domain 1
ComponentsCervical EMMPRIN
KeywordsCELL ADHESION / EMMPRIN / CD147 / dimerization / beta-strand swapping
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / response to cAMP / embryo implantation / photoreceptor inner segment / Degradation of the extracellular matrix / neutrophil chemotaxis / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Basigin / Basigin (Ok blood group), isoform CRA_a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, J. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2009
Title: Structure of the EMMPRIN N-terminal domain 1: Dimerization via beta-strand swapping.
Authors: Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T. / Wu, S.J. / Beil, E. / Baker, A. / Swencki-Underwood, B. / Zhao, Y. / Sprenkle, J. / Dixon, K. / Sweet, R. / Gilliland, G.L.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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: Cervical EMMPRIN
B: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)21,1172
Polymers21,1172
Non-polymers00
Water21612
1
A: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)10,5591
Polymers10,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)10,5591
Polymers10,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.480, 83.480, 49.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 25:44 or resseq 49:94 ) and backbone
211chain B and (resseq 25:44 or resseq 49:94 ) and backbone
112chain A and (resseq 95:102 )
212chain B and (resseq 95:102 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.293423, 0.758542, 0.581822), (0.799755, -0.5282, 0.285302), (0.523732, 0.381601, -0.761633)55.662899, -84.221199, -10.705
3given(0.273648, 0.860403, 0.429911), (0.782433, -0.459087, 0.420759), (0.559388, 0.221237, -0.798836)59.435699, -81.3843, -17.5993

-
Components

#1: Protein Cervical EMMPRIN


Mass: 10558.675 Da / Num. of mol.: 2 / Mutation: A19D, N44D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hEMMPRIN, BSG, hCG_20562 / Plasmid: pCEP4 / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo Sapiens (human) / References: UniProt: Q54A51, UniProt: P35613*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.2 M sodium formate, 3% MPD, 0.1 M sodium citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 7, 2007 / Details: Osmic VariMax Confocal
RadiationMonochromator: Osmic VariMax Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→42 Å / Num. all: 7149 / Num. obs: 7149 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.4 % / Biso Wilson estimate: 95.5 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.591 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 3B5H
Resolution: 2.5→29.237 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.98 / σ(F): 1.34 / Phase error: 35.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 335 4.71 %
Rwork0.2273 --
obs0.2287 7117 99.69 %
all-7117 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.124 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 90.571 Å2
Baniso -1Baniso -2Baniso -3
1--5.601 Å20 Å20 Å2
2---5.601 Å20 Å2
3---11.202 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 12 1241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091253
X-RAY DIFFRACTIONf_angle_d1.3241696
X-RAY DIFFRACTIONf_dihedral_angle_d18.637438
X-RAY DIFFRACTIONf_chiral_restr0.101199
X-RAY DIFFRACTIONf_plane_restr0.006214
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A268X-RAY DIFFRACTIONPOSITIONAL
12B268X-RAY DIFFRACTIONPOSITIONAL0.068
21A59X-RAY DIFFRACTIONPOSITIONAL
22B59X-RAY DIFFRACTIONPOSITIONAL0.091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.14960.39441610.27663340X-RAY DIFFRACTION100
3.1496-29.23950.22931740.21283442X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.58452.30242.88486.13610.59236.55070.1787-0.29920.42180.2596-0.34790.59210.1287-0.23090.23450.3509-0.05680.00390.3689-0.05620.39823.4296-29.92896.6966
20.3274-1.3356-0.18214.79880.68675.5898-0.40380.2715-0.6876-0.349-0.5688-1.7738-0.14420.01160.37170.2556-0.04630.41050.4241-0.04190.7674
34.91821.79231.87390.3487-1.38813.60920.041-0.01120.20880.00030.3821-0.23181.3301-0.2757-0.60610.876-0.1837-0.45380.61470.08920.8182
45.19071.90141.05562.0897-0.37915.3089-0.1157-0.1815-0.7891-0.21890.2262-0.70620.5060.30030.03750.4732-0.04440.15330.38850.07150.6262
59.16530.540.14788.91912.3042-0.967-0.5095-0.6743-0.35570.81790.3116-1.55550.7630.512-0.07860.4863-0.1870.03570.4733-0.17630.304
Refinement TLS groupSelection details: chain B and resid 93:103

+
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