[English] 日本語
Yorodumi
- PDB-1cls: CROSS-LINKED HUMAN HEMOGLOBIN DEOXY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cls
TitleCROSS-LINKED HUMAN HEMOGLOBIN DEOXY
Components(HEMOGLOBIN) x 2
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN / HUMAN / DEOXY / CROSS-LINKED
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SEBACIC ACID / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJi, X. / Fronticelli, C. / Bucci, E. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1996
Title: Positive and negative cooperativities at subsequent steps of oxygenation regulate the allosteric behavior of multistate sebacylhemoglobin.
Authors: Bucci, E. / Razynska, A. / Kwansa, H. / Gryczynski, Z. / Collins, J.H. / Fronticelli, C. / Unger, R. / Braxenthaler, M. / Moult, J. / Ji, X. / Gilliland, G.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Chloride Ion Independence of the Bohr Effect in a Mutant Human Hemoglobin Beta (V1M+H2Deleted)
Authors: Fronticelli, C. / Pechik, I. / Brinigar, W.S. / Kowalczyk, J. / Gilliland, G.L.
History
DepositionAug 29, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
C: HEMOGLOBIN
D: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,97313
Polymers62,0814
Non-polymers2,8929
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-132 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 82.470, 53.300
Angle α, β, γ (deg.)90.00, 99.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein HEMOGLOBIN / DECHB


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PURIFIED FROM OUTDATED BLOOD OBTAINED FROM THE BLOOD BANK OF THE UNIVERSITY OF MARYLAND
Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / Tissue: BLOOD / References: UniProt: P69905
#2: Protein HEMOGLOBIN / DECHB


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PURIFIED FROM OUTDATED BLOOD OBTAINED FROM THE BLOOD BANK OF THE UNIVERSITY OF MARYLAND
Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / Tissue: BLOOD / References: UniProt: P68871

-
Non-polymers , 5 types, 487 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DEC / SEBACIC ACID


Mass: 202.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 39 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 Mammonium phosphate11
21 g/dLprotein11

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 42167 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.58 % / Rmerge(I) obs: 0.09

-
Processing

Software
NameClassification
GPRLSArefinement
XENGENdata reduction
RefinementResolution: 1.9→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.168 -
obs-33545
Displacement parametersBiso mean: 19.95 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 196 478 5058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0390.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7291
X-RAY DIFFRACTIONp_mcangle_it1.1891.5
X-RAY DIFFRACTIONp_scbond_it1.5151.5
X-RAY DIFFRACTIONp_scangle_it2.3192
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr0.20.2
X-RAY DIFFRACTIONp_singtor_nbd0.2760.3
X-RAY DIFFRACTIONp_multtor_nbd0.1910.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2260.3
X-RAY DIFFRACTIONp_planar_tor3.55
X-RAY DIFFRACTIONp_staggered_tor17.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.815
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_planar_d0.042
X-RAY DIFFRACTIONp_plane_restr0.023
X-RAY DIFFRACTIONp_chiral_restr0.206
X-RAY DIFFRACTIONp_mcbond_it0.794
X-RAY DIFFRACTIONp_scbond_it1.628
X-RAY DIFFRACTIONp_mcangle_it1.237
X-RAY DIFFRACTIONp_scangle_it2.431

+
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