[English] 日本語
Yorodumi
- PDB-1gzl: Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gzl
TitleCrystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket
Components
  • ENVELOPE GLYCOPROTEIN GP41
  • FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
KeywordsGLYCOPROTEIN / HIV ENTRY / INHIBITOR / CROSS-LINK / GP41 / COILED COIL
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Synthesis and processing of ENV and VPU / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / symbiont-mediated evasion of host immune response / mediator complex binding / positive regulation of establishment of T cell polarity ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Synthesis and processing of ENV and VPU / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / symbiont-mediated evasion of host immune response / mediator complex binding / positive regulation of establishment of T cell polarity / Alpha-defensins / Oxidative Stress Induced Senescence / Dectin-2 family / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Binding and entry of HIV virion / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cellular response to amino acid starvation / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / clathrin-dependent endocytosis of virus by host cell / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / viral protein processing / RNA polymerase II cis-regulatory region sequence-specific DNA binding / receptor ligand activity / DNA-binding transcription factor activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane
Similarity search - Function
: / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Envelope glycoprotein Gp160 / Retroviral envelope protein ...: / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PENTANE-1,5-DIAMINE / General control transcription factor GCN4 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
HUMAN IMMUNODEFICIENCY VIRUS 1
HUMAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSia, S.K. / Carr, P.A. / Cochran, A.G. / Malashkevich, V.M. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Short Constrained Peptides that Inhibit HIV-1 Entry
Authors: Sia, S.K. / Carr, P.A. / Cochran, A.G. / Malashkevich, V.M. / Kim, P.S.
History
DepositionMay 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2002Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 2019Group: Derived calculations / Other / Source and taxonomy
Category: pdbx_database_status / pdbx_entity_src_syn / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
B: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
C: ENVELOPE GLYCOPROTEIN GP41
D: ENVELOPE GLYCOPROTEIN GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5548
Polymers14,2794
Non-polymers2754
Water1,38777
1
A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
C: ENVELOPE GLYCOPROTEIN GP41
hetero molecules

A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
C: ENVELOPE GLYCOPROTEIN GP41
hetero molecules

A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
C: ENVELOPE GLYCOPROTEIN GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,83112
Polymers21,4186
Non-polymers4136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
Buried area9780 Å2
ΔGint-84.2 kcal/mol
Surface area10500 Å2
MethodPISA
2
B: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
D: ENVELOPE GLYCOPROTEIN GP41
hetero molecules

B: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
D: ENVELOPE GLYCOPROTEIN GP41
hetero molecules

B: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI
D: ENVELOPE GLYCOPROTEIN GP41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,83112
Polymers21,4186
Non-polymers4136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area9990 Å2
ΔGint-81.4 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.358, 38.358, 169.695
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1046-

CL

21B-1046-

CL

DetailsAND CHAINS B AND D). APPLYING CRYSTAL SYMMETRY GENERATES TWO TRIMERS OF HETERODIMERS (HEXAMERS).

-
Components

#1: Protein/peptide FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GENERAL CONTROL PROTEIN GCN4-PIQI


Mass: 5468.566 Da / Num. of mol.: 2
Fragment: GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED
Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1
References: UniProt: P03069, UniProt: P04578
#2: Protein/peptide ENVELOPE GLYCOPROTEIN GP41 / C14LINKMID


Mass: 1670.710 Da / Num. of mol.: 2 / Fragment: RESIDUES 628-639 / Mutation: YES / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: P04578
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION MET 629 GLU CHAINS C AND D ENGINEERED MUTATION ASN 636 GLU CHAINS C AND D
Has protein modificationY
Sequence detailsIN CHAINS C AND D, MET 629 AND ASN 636 ARE MUTATED TO GLUTAMIC ACID. A DIAMINOPENTANE GROUP LINKS ...IN CHAINS C AND D, MET 629 AND ASN 636 ARE MUTATED TO GLUTAMIC ACID. A DIAMINOPENTANE GROUP LINKS GLU 629 AND GLU 636

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.6 %
Crystal growpH: 8.6 / Details: 16% ISOPROPANOL, 0.1 M TRIS, PH 8.6, 1 M (NH4)2SO4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 mMprotein1drop
216 %isopropanol1reservoir
30.1 MTris1reservoirpH8.6
41 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 19, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 59821 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.044 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 7.2 / % possible all: 69.5
Reflection
*PLUS
Highest resolution: 1.86 Å / Num. obs: 11190 / % possible obs: 94.3 % / Num. measured all: 59821 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 80.2 % / Rmerge(I) obs: 0.15

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNBOUND IQN17 AND A MODEL OF C14LINKMID BOUND TO THE HYDROPHOBIC POCKET

Resolution: 1.8→19.58 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 505253.07 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FINAL REFINEMENT IS AFTER DETWINNING DATA. 529 REFLECTIONS WERE REJECTED BY CNS AFTER MEROHEDRAL DETWINNING. THE THREE CHAINS OF THE TRIMER ARE RELATED BY CRYSTALLOGRAPHIC SYMMETRY. TO ...Details: FINAL REFINEMENT IS AFTER DETWINNING DATA. 529 REFLECTIONS WERE REJECTED BY CNS AFTER MEROHEDRAL DETWINNING. THE THREE CHAINS OF THE TRIMER ARE RELATED BY CRYSTALLOGRAPHIC SYMMETRY. TO GENERATE THE TRIMER, APPLY SYMMETRY TRANSFORMATIONS. THE FINAL MODEL CONSISTS OF ALL RESIDUES EXCEPT FOR THE TWO N-TERMINAL RESIDUES OF C14LINKMID, WHICH ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 685 6.4 %RANDOM
Rwork0.208 ---
obs0.208 10672 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 97.565 Å2 / ksol: 0.428224 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 16 77 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 76 6.2 %
Rwork0.296 1143 -
obs--55.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_D.PARAMPROTEIN_GN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Highest resolution: 1.86 Å / Lowest resolution: 20 Å / Num. reflection obs: 10090 / Num. reflection Rfree: 687
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.297

+
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